[805] | 1 | // |
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| 2 | // C++ Implementation: Scantable |
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| 3 | // |
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| 4 | // Description: |
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| 5 | // |
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| 6 | // |
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| 7 | // Author: Malte Marquarding <asap@atnf.csiro.au>, (C) 2005 |
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| 8 | // |
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| 9 | // Copyright: See COPYING file that comes with this distribution |
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| 10 | // |
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| 11 | // |
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[206] | 12 | #include <map> |
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[2591] | 13 | #include <sys/time.h> |
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[206] | 14 | |
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[2186] | 15 | #include <atnf/PKSIO/SrcType.h> |
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| 16 | |
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[125] | 17 | #include <casa/aips.h> |
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[2186] | 18 | #include <casa/iomanip.h> |
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[80] | 19 | #include <casa/iostream.h> |
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[2186] | 20 | #include <casa/OS/File.h> |
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[805] | 21 | #include <casa/OS/Path.h> |
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[2658] | 22 | #include <casa/Logging/LogIO.h> |
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[80] | 23 | #include <casa/Arrays/Array.h> |
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[2186] | 24 | #include <casa/Arrays/ArrayAccessor.h> |
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| 25 | #include <casa/Arrays/ArrayLogical.h> |
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[80] | 26 | #include <casa/Arrays/ArrayMath.h> |
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| 27 | #include <casa/Arrays/MaskArrMath.h> |
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[2186] | 28 | #include <casa/Arrays/Slice.h> |
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[1325] | 29 | #include <casa/Arrays/Vector.h> |
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[455] | 30 | #include <casa/Arrays/VectorSTLIterator.h> |
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[418] | 31 | #include <casa/BasicMath/Math.h> |
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[504] | 32 | #include <casa/BasicSL/Constants.h> |
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[2186] | 33 | #include <casa/Containers/RecordField.h> |
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| 34 | #include <casa/Logging/LogIO.h> |
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[286] | 35 | #include <casa/Quanta/MVAngle.h> |
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[2186] | 36 | #include <casa/Quanta/MVTime.h> |
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[902] | 37 | #include <casa/Utilities/GenSort.h> |
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[2] | 38 | |
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[2186] | 39 | #include <coordinates/Coordinates/CoordinateUtil.h> |
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[2] | 40 | |
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[1325] | 41 | // needed to avoid error in .tcc |
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| 42 | #include <measures/Measures/MCDirection.h> |
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| 43 | // |
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| 44 | #include <measures/Measures/MDirection.h> |
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[2186] | 45 | #include <measures/Measures/MEpoch.h> |
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[80] | 46 | #include <measures/Measures/MFrequency.h> |
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[2186] | 47 | #include <measures/Measures/MeasRef.h> |
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| 48 | #include <measures/Measures/MeasTable.h> |
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| 49 | #include <measures/TableMeasures/ScalarMeasColumn.h> |
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| 50 | #include <measures/TableMeasures/TableMeasDesc.h> |
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[805] | 51 | #include <measures/TableMeasures/TableMeasRefDesc.h> |
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| 52 | #include <measures/TableMeasures/TableMeasValueDesc.h> |
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[2] | 53 | |
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[2186] | 54 | #include <tables/Tables/ArrColDesc.h> |
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| 55 | #include <tables/Tables/ExprNode.h> |
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| 56 | #include <tables/Tables/ScaColDesc.h> |
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| 57 | #include <tables/Tables/SetupNewTab.h> |
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| 58 | #include <tables/Tables/TableCopy.h> |
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| 59 | #include <tables/Tables/TableDesc.h> |
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| 60 | #include <tables/Tables/TableIter.h> |
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| 61 | #include <tables/Tables/TableParse.h> |
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| 62 | #include <tables/Tables/TableRecord.h> |
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| 63 | #include <tables/Tables/TableRow.h> |
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| 64 | #include <tables/Tables/TableVector.h> |
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| 65 | |
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| 66 | #include "MathUtils.h" |
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| 67 | #include "STAttr.h" |
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[2737] | 68 | #include "STBaselineTable.h" |
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[2186] | 69 | #include "STLineFinder.h" |
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| 70 | #include "STPolCircular.h" |
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[896] | 71 | #include "STPolLinear.h" |
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[913] | 72 | #include "STPolStokes.h" |
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[2321] | 73 | #include "STUpgrade.h" |
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[2666] | 74 | #include "STFitter.h" |
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[2186] | 75 | #include "Scantable.h" |
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[2] | 76 | |
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[2462] | 77 | #define debug 1 |
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| 78 | |
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[125] | 79 | using namespace casa; |
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[2] | 80 | |
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[805] | 81 | namespace asap { |
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| 82 | |
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[896] | 83 | std::map<std::string, STPol::STPolFactory *> Scantable::factories_; |
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| 84 | |
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| 85 | void Scantable::initFactories() { |
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| 86 | if ( factories_.empty() ) { |
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| 87 | Scantable::factories_["linear"] = &STPolLinear::myFactory; |
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[1323] | 88 | Scantable::factories_["circular"] = &STPolCircular::myFactory; |
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[913] | 89 | Scantable::factories_["stokes"] = &STPolStokes::myFactory; |
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[896] | 90 | } |
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| 91 | } |
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| 92 | |
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[805] | 93 | Scantable::Scantable(Table::TableType ttype) : |
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[852] | 94 | type_(ttype) |
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[206] | 95 | { |
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[896] | 96 | initFactories(); |
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[805] | 97 | setupMainTable(); |
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[2346] | 98 | freqTable_ = STFrequencies(*this); |
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| 99 | table_.rwKeywordSet().defineTable("FREQUENCIES", freqTable_.table()); |
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[852] | 100 | weatherTable_ = STWeather(*this); |
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[805] | 101 | table_.rwKeywordSet().defineTable("WEATHER", weatherTable_.table()); |
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[852] | 102 | focusTable_ = STFocus(*this); |
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[805] | 103 | table_.rwKeywordSet().defineTable("FOCUS", focusTable_.table()); |
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[852] | 104 | tcalTable_ = STTcal(*this); |
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[805] | 105 | table_.rwKeywordSet().defineTable("TCAL", tcalTable_.table()); |
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[852] | 106 | moleculeTable_ = STMolecules(*this); |
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[805] | 107 | table_.rwKeywordSet().defineTable("MOLECULES", moleculeTable_.table()); |
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[860] | 108 | historyTable_ = STHistory(*this); |
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| 109 | table_.rwKeywordSet().defineTable("HISTORY", historyTable_.table()); |
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[959] | 110 | fitTable_ = STFit(*this); |
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| 111 | table_.rwKeywordSet().defineTable("FIT", fitTable_.table()); |
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[1881] | 112 | table_.tableInfo().setType( "Scantable" ) ; |
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[805] | 113 | originalTable_ = table_; |
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[322] | 114 | attach(); |
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[18] | 115 | } |
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[206] | 116 | |
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[805] | 117 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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[852] | 118 | type_(ttype) |
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[206] | 119 | { |
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[896] | 120 | initFactories(); |
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[1819] | 121 | |
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[865] | 122 | Table tab(name, Table::Update); |
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[1009] | 123 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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[483] | 124 | if (version != version_) { |
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[2321] | 125 | STUpgrade upgrader(version_); |
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[2162] | 126 | LogIO os( LogOrigin( "Scantable" ) ) ; |
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| 127 | os << LogIO::WARN |
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[2321] | 128 | << name << " data format version " << version |
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| 129 | << " is deprecated" << endl |
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| 130 | << "Running upgrade."<< endl |
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[2162] | 131 | << LogIO::POST ; |
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[2321] | 132 | std::string outname = upgrader.upgrade(name); |
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[2332] | 133 | if ( outname != name ) { |
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| 134 | os << LogIO::WARN |
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| 135 | << "Data will be loaded from " << outname << " instead of " |
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| 136 | << name << LogIO::POST ; |
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| 137 | tab = Table(outname, Table::Update ) ; |
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| 138 | } |
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[483] | 139 | } |
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[1009] | 140 | if ( type_ == Table::Memory ) { |
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[852] | 141 | table_ = tab.copyToMemoryTable(generateName()); |
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[1009] | 142 | } else { |
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[805] | 143 | table_ = tab; |
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[1009] | 144 | } |
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[1881] | 145 | table_.tableInfo().setType( "Scantable" ) ; |
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[1009] | 146 | |
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[859] | 147 | attachSubtables(); |
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[805] | 148 | originalTable_ = table_; |
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[329] | 149 | attach(); |
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[2] | 150 | } |
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[1819] | 151 | /* |
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| 152 | Scantable::Scantable(const std::string& name, Table::TableType ttype) : |
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| 153 | type_(ttype) |
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| 154 | { |
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| 155 | initFactories(); |
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| 156 | Table tab(name, Table::Update); |
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| 157 | uInt version = tab.keywordSet().asuInt("VERSION"); |
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| 158 | if (version != version_) { |
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| 159 | throw(AipsError("Unsupported version of ASAP file.")); |
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| 160 | } |
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| 161 | if ( type_ == Table::Memory ) { |
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| 162 | table_ = tab.copyToMemoryTable(generateName()); |
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| 163 | } else { |
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| 164 | table_ = tab; |
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| 165 | } |
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[2] | 166 | |
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[1819] | 167 | attachSubtables(); |
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| 168 | originalTable_ = table_; |
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| 169 | attach(); |
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| 170 | } |
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| 171 | */ |
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| 172 | |
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[2658] | 173 | Scantable::Scantable( const Scantable& other, bool clear ) |
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[206] | 174 | { |
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[805] | 175 | // with or without data |
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[859] | 176 | String newname = String(generateName()); |
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[865] | 177 | type_ = other.table_.tableType(); |
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[859] | 178 | if ( other.table_.tableType() == Table::Memory ) { |
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| 179 | if ( clear ) { |
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| 180 | table_ = TableCopy::makeEmptyMemoryTable(newname, |
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| 181 | other.table_, True); |
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| 182 | } else |
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| 183 | table_ = other.table_.copyToMemoryTable(newname); |
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[16] | 184 | } else { |
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[915] | 185 | other.table_.deepCopy(newname, Table::New, False, |
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| 186 | other.table_.endianFormat(), |
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[865] | 187 | Bool(clear)); |
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| 188 | table_ = Table(newname, Table::Update); |
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| 189 | table_.markForDelete(); |
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| 190 | } |
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[1881] | 191 | table_.tableInfo().setType( "Scantable" ) ; |
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[1111] | 192 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
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[915] | 193 | if ( clear ) copySubtables(other); |
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[859] | 194 | attachSubtables(); |
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[805] | 195 | originalTable_ = table_; |
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[322] | 196 | attach(); |
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[2] | 197 | } |
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| 198 | |
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[865] | 199 | void Scantable::copySubtables(const Scantable& other) { |
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| 200 | Table t = table_.rwKeywordSet().asTable("FREQUENCIES"); |
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[2346] | 201 | TableCopy::copyRows(t, other.freqTable_.table()); |
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[865] | 202 | t = table_.rwKeywordSet().asTable("FOCUS"); |
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| 203 | TableCopy::copyRows(t, other.focusTable_.table()); |
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| 204 | t = table_.rwKeywordSet().asTable("WEATHER"); |
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| 205 | TableCopy::copyRows(t, other.weatherTable_.table()); |
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| 206 | t = table_.rwKeywordSet().asTable("TCAL"); |
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| 207 | TableCopy::copyRows(t, other.tcalTable_.table()); |
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| 208 | t = table_.rwKeywordSet().asTable("MOLECULES"); |
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| 209 | TableCopy::copyRows(t, other.moleculeTable_.table()); |
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| 210 | t = table_.rwKeywordSet().asTable("HISTORY"); |
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| 211 | TableCopy::copyRows(t, other.historyTable_.table()); |
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[972] | 212 | t = table_.rwKeywordSet().asTable("FIT"); |
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| 213 | TableCopy::copyRows(t, other.fitTable_.table()); |
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[865] | 214 | } |
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| 215 | |
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[859] | 216 | void Scantable::attachSubtables() |
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| 217 | { |
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[2346] | 218 | freqTable_ = STFrequencies(table_); |
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[859] | 219 | focusTable_ = STFocus(table_); |
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| 220 | weatherTable_ = STWeather(table_); |
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| 221 | tcalTable_ = STTcal(table_); |
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| 222 | moleculeTable_ = STMolecules(table_); |
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[860] | 223 | historyTable_ = STHistory(table_); |
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[972] | 224 | fitTable_ = STFit(table_); |
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[859] | 225 | } |
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| 226 | |
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[805] | 227 | Scantable::~Scantable() |
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[206] | 228 | { |
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[2] | 229 | } |
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| 230 | |
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[805] | 231 | void Scantable::setupMainTable() |
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[206] | 232 | { |
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[805] | 233 | TableDesc td("", "1", TableDesc::Scratch); |
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| 234 | td.comment() = "An ASAP Scantable"; |
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[1009] | 235 | td.rwKeywordSet().define("VERSION", uInt(version_)); |
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[2] | 236 | |
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[805] | 237 | // n Cycles |
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| 238 | td.addColumn(ScalarColumnDesc<uInt>("SCANNO")); |
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| 239 | // new index every nBeam x nIF x nPol |
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| 240 | td.addColumn(ScalarColumnDesc<uInt>("CYCLENO")); |
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[2] | 241 | |
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[805] | 242 | td.addColumn(ScalarColumnDesc<uInt>("BEAMNO")); |
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| 243 | td.addColumn(ScalarColumnDesc<uInt>("IFNO")); |
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[972] | 244 | // linear, circular, stokes |
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[805] | 245 | td.rwKeywordSet().define("POLTYPE", String("linear")); |
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| 246 | td.addColumn(ScalarColumnDesc<uInt>("POLNO")); |
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[138] | 247 | |
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[805] | 248 | td.addColumn(ScalarColumnDesc<uInt>("FREQ_ID")); |
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| 249 | td.addColumn(ScalarColumnDesc<uInt>("MOLECULE_ID")); |
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[80] | 250 | |
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[1819] | 251 | ScalarColumnDesc<Int> refbeamnoColumn("REFBEAMNO"); |
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| 252 | refbeamnoColumn.setDefault(Int(-1)); |
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| 253 | td.addColumn(refbeamnoColumn); |
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| 254 | |
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| 255 | ScalarColumnDesc<uInt> flagrowColumn("FLAGROW"); |
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| 256 | flagrowColumn.setDefault(uInt(0)); |
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| 257 | td.addColumn(flagrowColumn); |
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| 258 | |
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[805] | 259 | td.addColumn(ScalarColumnDesc<Double>("TIME")); |
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| 260 | TableMeasRefDesc measRef(MEpoch::UTC); // UTC as default |
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| 261 | TableMeasValueDesc measVal(td, "TIME"); |
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| 262 | TableMeasDesc<MEpoch> mepochCol(measVal, measRef); |
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| 263 | mepochCol.write(td); |
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[483] | 264 | |
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[805] | 265 | td.addColumn(ScalarColumnDesc<Double>("INTERVAL")); |
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| 266 | |
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[2] | 267 | td.addColumn(ScalarColumnDesc<String>("SRCNAME")); |
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[805] | 268 | // Type of source (on=0, off=1, other=-1) |
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[1503] | 269 | ScalarColumnDesc<Int> stypeColumn("SRCTYPE"); |
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| 270 | stypeColumn.setDefault(Int(-1)); |
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| 271 | td.addColumn(stypeColumn); |
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[805] | 272 | td.addColumn(ScalarColumnDesc<String>("FIELDNAME")); |
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| 273 | |
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| 274 | //The actual Data Vectors |
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[2] | 275 | td.addColumn(ArrayColumnDesc<Float>("SPECTRA")); |
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| 276 | td.addColumn(ArrayColumnDesc<uChar>("FLAGTRA")); |
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[89] | 277 | td.addColumn(ArrayColumnDesc<Float>("TSYS")); |
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[805] | 278 | |
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| 279 | td.addColumn(ArrayColumnDesc<Double>("DIRECTION", |
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| 280 | IPosition(1,2), |
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| 281 | ColumnDesc::Direct)); |
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| 282 | TableMeasRefDesc mdirRef(MDirection::J2000); // default |
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| 283 | TableMeasValueDesc tmvdMDir(td, "DIRECTION"); |
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| 284 | // the TableMeasDesc gives the column a type |
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| 285 | TableMeasDesc<MDirection> mdirCol(tmvdMDir, mdirRef); |
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[987] | 286 | // a uder set table type e.g. GALCTIC, B1950 ... |
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| 287 | td.rwKeywordSet().define("DIRECTIONREF", String("J2000")); |
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[805] | 288 | // writing create the measure column |
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| 289 | mdirCol.write(td); |
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[923] | 290 | td.addColumn(ScalarColumnDesc<Float>("AZIMUTH")); |
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| 291 | td.addColumn(ScalarColumnDesc<Float>("ELEVATION")); |
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[1047] | 292 | td.addColumn(ScalarColumnDesc<Float>("OPACITY")); |
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[105] | 293 | |
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[805] | 294 | td.addColumn(ScalarColumnDesc<uInt>("TCAL_ID")); |
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[972] | 295 | ScalarColumnDesc<Int> fitColumn("FIT_ID"); |
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[973] | 296 | fitColumn.setDefault(Int(-1)); |
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[972] | 297 | td.addColumn(fitColumn); |
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[805] | 298 | |
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| 299 | td.addColumn(ScalarColumnDesc<uInt>("FOCUS_ID")); |
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| 300 | td.addColumn(ScalarColumnDesc<uInt>("WEATHER_ID")); |
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| 301 | |
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[999] | 302 | // columns which just get dragged along, as they aren't used in asap |
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| 303 | td.addColumn(ScalarColumnDesc<Double>("SRCVELOCITY")); |
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| 304 | td.addColumn(ArrayColumnDesc<Double>("SRCPROPERMOTION")); |
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| 305 | td.addColumn(ArrayColumnDesc<Double>("SRCDIRECTION")); |
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| 306 | td.addColumn(ArrayColumnDesc<Double>("SCANRATE")); |
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| 307 | |
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[805] | 308 | td.rwKeywordSet().define("OBSMODE", String("")); |
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| 309 | |
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[418] | 310 | // Now create Table SetUp from the description. |
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[859] | 311 | SetupNewTable aNewTab(generateName(), td, Table::Scratch); |
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[852] | 312 | table_ = Table(aNewTab, type_, 0); |
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[805] | 313 | originalTable_ = table_; |
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| 314 | } |
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[418] | 315 | |
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[805] | 316 | void Scantable::attach() |
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[455] | 317 | { |
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[805] | 318 | timeCol_.attach(table_, "TIME"); |
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| 319 | srcnCol_.attach(table_, "SRCNAME"); |
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[1068] | 320 | srctCol_.attach(table_, "SRCTYPE"); |
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[805] | 321 | specCol_.attach(table_, "SPECTRA"); |
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| 322 | flagsCol_.attach(table_, "FLAGTRA"); |
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[865] | 323 | tsysCol_.attach(table_, "TSYS"); |
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[805] | 324 | cycleCol_.attach(table_,"CYCLENO"); |
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| 325 | scanCol_.attach(table_, "SCANNO"); |
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| 326 | beamCol_.attach(table_, "BEAMNO"); |
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[847] | 327 | ifCol_.attach(table_, "IFNO"); |
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| 328 | polCol_.attach(table_, "POLNO"); |
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[805] | 329 | integrCol_.attach(table_, "INTERVAL"); |
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| 330 | azCol_.attach(table_, "AZIMUTH"); |
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| 331 | elCol_.attach(table_, "ELEVATION"); |
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| 332 | dirCol_.attach(table_, "DIRECTION"); |
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| 333 | fldnCol_.attach(table_, "FIELDNAME"); |
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| 334 | rbeamCol_.attach(table_, "REFBEAMNO"); |
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[455] | 335 | |
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[1730] | 336 | mweatheridCol_.attach(table_,"WEATHER_ID"); |
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[805] | 337 | mfitidCol_.attach(table_,"FIT_ID"); |
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| 338 | mfreqidCol_.attach(table_, "FREQ_ID"); |
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| 339 | mtcalidCol_.attach(table_, "TCAL_ID"); |
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| 340 | mfocusidCol_.attach(table_, "FOCUS_ID"); |
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| 341 | mmolidCol_.attach(table_, "MOLECULE_ID"); |
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[1819] | 342 | |
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| 343 | //Add auxiliary column for row-based flagging (CAS-1433 Wataru Kawasaki) |
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| 344 | attachAuxColumnDef(flagrowCol_, "FLAGROW", 0); |
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| 345 | |
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[455] | 346 | } |
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| 347 | |
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[1819] | 348 | template<class T, class T2> |
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| 349 | void Scantable::attachAuxColumnDef(ScalarColumn<T>& col, |
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| 350 | const String& colName, |
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| 351 | const T2& defValue) |
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| 352 | { |
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| 353 | try { |
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| 354 | col.attach(table_, colName); |
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| 355 | } catch (TableError& err) { |
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| 356 | String errMesg = err.getMesg(); |
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| 357 | if (errMesg == "Table column " + colName + " is unknown") { |
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| 358 | table_.addColumn(ScalarColumnDesc<T>(colName)); |
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| 359 | col.attach(table_, colName); |
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| 360 | col.fillColumn(static_cast<T>(defValue)); |
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| 361 | } else { |
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| 362 | throw; |
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| 363 | } |
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| 364 | } catch (...) { |
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| 365 | throw; |
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| 366 | } |
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| 367 | } |
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| 368 | |
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| 369 | template<class T, class T2> |
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| 370 | void Scantable::attachAuxColumnDef(ArrayColumn<T>& col, |
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| 371 | const String& colName, |
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| 372 | const Array<T2>& defValue) |
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| 373 | { |
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| 374 | try { |
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| 375 | col.attach(table_, colName); |
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| 376 | } catch (TableError& err) { |
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| 377 | String errMesg = err.getMesg(); |
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| 378 | if (errMesg == "Table column " + colName + " is unknown") { |
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| 379 | table_.addColumn(ArrayColumnDesc<T>(colName)); |
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| 380 | col.attach(table_, colName); |
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| 381 | |
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| 382 | int size = 0; |
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| 383 | ArrayIterator<T2>& it = defValue.begin(); |
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| 384 | while (it != defValue.end()) { |
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| 385 | ++size; |
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| 386 | ++it; |
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| 387 | } |
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| 388 | IPosition ip(1, size); |
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| 389 | Array<T>& arr(ip); |
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| 390 | for (int i = 0; i < size; ++i) |
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| 391 | arr[i] = static_cast<T>(defValue[i]); |
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| 392 | |
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| 393 | col.fillColumn(arr); |
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| 394 | } else { |
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| 395 | throw; |
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| 396 | } |
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| 397 | } catch (...) { |
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| 398 | throw; |
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| 399 | } |
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| 400 | } |
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| 401 | |
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[901] | 402 | void Scantable::setHeader(const STHeader& sdh) |
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[206] | 403 | { |
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[18] | 404 | table_.rwKeywordSet().define("nIF", sdh.nif); |
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| 405 | table_.rwKeywordSet().define("nBeam", sdh.nbeam); |
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| 406 | table_.rwKeywordSet().define("nPol", sdh.npol); |
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| 407 | table_.rwKeywordSet().define("nChan", sdh.nchan); |
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| 408 | table_.rwKeywordSet().define("Observer", sdh.observer); |
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| 409 | table_.rwKeywordSet().define("Project", sdh.project); |
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| 410 | table_.rwKeywordSet().define("Obstype", sdh.obstype); |
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| 411 | table_.rwKeywordSet().define("AntennaName", sdh.antennaname); |
---|
| 412 | table_.rwKeywordSet().define("AntennaPosition", sdh.antennaposition); |
---|
| 413 | table_.rwKeywordSet().define("Equinox", sdh.equinox); |
---|
| 414 | table_.rwKeywordSet().define("FreqRefFrame", sdh.freqref); |
---|
| 415 | table_.rwKeywordSet().define("FreqRefVal", sdh.reffreq); |
---|
| 416 | table_.rwKeywordSet().define("Bandwidth", sdh.bandwidth); |
---|
| 417 | table_.rwKeywordSet().define("UTC", sdh.utc); |
---|
[206] | 418 | table_.rwKeywordSet().define("FluxUnit", sdh.fluxunit); |
---|
| 419 | table_.rwKeywordSet().define("Epoch", sdh.epoch); |
---|
[905] | 420 | table_.rwKeywordSet().define("POLTYPE", sdh.poltype); |
---|
[50] | 421 | } |
---|
[21] | 422 | |
---|
[901] | 423 | STHeader Scantable::getHeader() const |
---|
[206] | 424 | { |
---|
[901] | 425 | STHeader sdh; |
---|
[21] | 426 | table_.keywordSet().get("nBeam",sdh.nbeam); |
---|
| 427 | table_.keywordSet().get("nIF",sdh.nif); |
---|
| 428 | table_.keywordSet().get("nPol",sdh.npol); |
---|
| 429 | table_.keywordSet().get("nChan",sdh.nchan); |
---|
| 430 | table_.keywordSet().get("Observer", sdh.observer); |
---|
| 431 | table_.keywordSet().get("Project", sdh.project); |
---|
| 432 | table_.keywordSet().get("Obstype", sdh.obstype); |
---|
| 433 | table_.keywordSet().get("AntennaName", sdh.antennaname); |
---|
| 434 | table_.keywordSet().get("AntennaPosition", sdh.antennaposition); |
---|
| 435 | table_.keywordSet().get("Equinox", sdh.equinox); |
---|
| 436 | table_.keywordSet().get("FreqRefFrame", sdh.freqref); |
---|
| 437 | table_.keywordSet().get("FreqRefVal", sdh.reffreq); |
---|
| 438 | table_.keywordSet().get("Bandwidth", sdh.bandwidth); |
---|
| 439 | table_.keywordSet().get("UTC", sdh.utc); |
---|
[206] | 440 | table_.keywordSet().get("FluxUnit", sdh.fluxunit); |
---|
| 441 | table_.keywordSet().get("Epoch", sdh.epoch); |
---|
[905] | 442 | table_.keywordSet().get("POLTYPE", sdh.poltype); |
---|
[21] | 443 | return sdh; |
---|
[18] | 444 | } |
---|
[805] | 445 | |
---|
[1360] | 446 | void Scantable::setSourceType( int stype ) |
---|
[1068] | 447 | { |
---|
| 448 | if ( stype < 0 || stype > 1 ) |
---|
| 449 | throw(AipsError("Illegal sourcetype.")); |
---|
| 450 | TableVector<Int> tabvec(table_, "SRCTYPE"); |
---|
| 451 | tabvec = Int(stype); |
---|
| 452 | } |
---|
| 453 | |
---|
[845] | 454 | bool Scantable::conformant( const Scantable& other ) |
---|
| 455 | { |
---|
| 456 | return this->getHeader().conformant(other.getHeader()); |
---|
| 457 | } |
---|
| 458 | |
---|
| 459 | |
---|
[50] | 460 | |
---|
[805] | 461 | std::string Scantable::formatSec(Double x) const |
---|
[206] | 462 | { |
---|
[105] | 463 | Double xcop = x; |
---|
| 464 | MVTime mvt(xcop/24./3600.); // make days |
---|
[365] | 465 | |
---|
[105] | 466 | if (x < 59.95) |
---|
[281] | 467 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_HM, 7)+"s"; |
---|
[745] | 468 | else if (x < 3599.95) |
---|
[281] | 469 | return String(" ") + mvt.string(MVTime::TIME_CLEAN_NO_H,7)+" "; |
---|
| 470 | else { |
---|
| 471 | ostringstream oss; |
---|
| 472 | oss << setw(2) << std::right << setprecision(1) << mvt.hour(); |
---|
| 473 | oss << ":" << mvt.string(MVTime::TIME_CLEAN_NO_H,7) << " "; |
---|
| 474 | return String(oss); |
---|
[745] | 475 | } |
---|
[105] | 476 | }; |
---|
| 477 | |
---|
[805] | 478 | std::string Scantable::formatDirection(const MDirection& md) const |
---|
[281] | 479 | { |
---|
| 480 | Vector<Double> t = md.getAngle(Unit(String("rad"))).getValue(); |
---|
| 481 | Int prec = 7; |
---|
| 482 | |
---|
[2575] | 483 | String ref = md.getRefString(); |
---|
[281] | 484 | MVAngle mvLon(t[0]); |
---|
| 485 | String sLon = mvLon.string(MVAngle::TIME,prec); |
---|
[987] | 486 | uInt tp = md.getRef().getType(); |
---|
| 487 | if (tp == MDirection::GALACTIC || |
---|
| 488 | tp == MDirection::SUPERGAL ) { |
---|
| 489 | sLon = mvLon(0.0).string(MVAngle::ANGLE_CLEAN,prec); |
---|
| 490 | } |
---|
[281] | 491 | MVAngle mvLat(t[1]); |
---|
| 492 | String sLat = mvLat.string(MVAngle::ANGLE+MVAngle::DIG2,prec); |
---|
[2575] | 493 | return ref + String(" ") + sLon + String(" ") + sLat; |
---|
[281] | 494 | } |
---|
| 495 | |
---|
| 496 | |
---|
[805] | 497 | std::string Scantable::getFluxUnit() const |
---|
[206] | 498 | { |
---|
[847] | 499 | return table_.keywordSet().asString("FluxUnit"); |
---|
[206] | 500 | } |
---|
| 501 | |
---|
[805] | 502 | void Scantable::setFluxUnit(const std::string& unit) |
---|
[218] | 503 | { |
---|
| 504 | String tmp(unit); |
---|
| 505 | Unit tU(tmp); |
---|
| 506 | if (tU==Unit("K") || tU==Unit("Jy")) { |
---|
| 507 | table_.rwKeywordSet().define(String("FluxUnit"), tmp); |
---|
| 508 | } else { |
---|
| 509 | throw AipsError("Illegal unit - must be compatible with Jy or K"); |
---|
| 510 | } |
---|
| 511 | } |
---|
| 512 | |
---|
[805] | 513 | void Scantable::setInstrument(const std::string& name) |
---|
[236] | 514 | { |
---|
[805] | 515 | bool throwIt = true; |
---|
[996] | 516 | // create an Instrument to see if this is valid |
---|
| 517 | STAttr::convertInstrument(name, throwIt); |
---|
[236] | 518 | String nameU(name); |
---|
| 519 | nameU.upcase(); |
---|
| 520 | table_.rwKeywordSet().define(String("AntennaName"), nameU); |
---|
| 521 | } |
---|
| 522 | |
---|
[1189] | 523 | void Scantable::setFeedType(const std::string& feedtype) |
---|
| 524 | { |
---|
| 525 | if ( Scantable::factories_.find(feedtype) == Scantable::factories_.end() ) { |
---|
| 526 | std::string msg = "Illegal feed type "+ feedtype; |
---|
| 527 | throw(casa::AipsError(msg)); |
---|
| 528 | } |
---|
| 529 | table_.rwKeywordSet().define(String("POLTYPE"), feedtype); |
---|
| 530 | } |
---|
| 531 | |
---|
[1743] | 532 | MPosition Scantable::getAntennaPosition() const |
---|
[805] | 533 | { |
---|
| 534 | Vector<Double> antpos; |
---|
| 535 | table_.keywordSet().get("AntennaPosition", antpos); |
---|
| 536 | MVPosition mvpos(antpos(0),antpos(1),antpos(2)); |
---|
| 537 | return MPosition(mvpos); |
---|
| 538 | } |
---|
[281] | 539 | |
---|
[805] | 540 | void Scantable::makePersistent(const std::string& filename) |
---|
| 541 | { |
---|
| 542 | String inname(filename); |
---|
| 543 | Path path(inname); |
---|
[1111] | 544 | /// @todo reindex SCANNO, recompute nbeam, nif, npol |
---|
[805] | 545 | inname = path.expandedName(); |
---|
[2030] | 546 | // 2011/03/04 TN |
---|
| 547 | // We can comment out this workaround since the essential bug is |
---|
| 548 | // fixed in casacore (r20889 in google code). |
---|
| 549 | table_.deepCopy(inname, Table::New); |
---|
| 550 | // // WORKAROUND !!! for Table bug |
---|
| 551 | // // Remove when fixed in casacore |
---|
| 552 | // if ( table_.tableType() == Table::Memory && !selector_.empty() ) { |
---|
| 553 | // Table tab = table_.copyToMemoryTable(generateName()); |
---|
| 554 | // tab.deepCopy(inname, Table::New); |
---|
| 555 | // tab.markForDelete(); |
---|
| 556 | // |
---|
| 557 | // } else { |
---|
| 558 | // table_.deepCopy(inname, Table::New); |
---|
| 559 | // } |
---|
[805] | 560 | } |
---|
| 561 | |
---|
[837] | 562 | int Scantable::nbeam( int scanno ) const |
---|
[805] | 563 | { |
---|
| 564 | if ( scanno < 0 ) { |
---|
| 565 | Int n; |
---|
| 566 | table_.keywordSet().get("nBeam",n); |
---|
| 567 | return int(n); |
---|
[105] | 568 | } else { |
---|
[805] | 569 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 570 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 571 | ROTableRow row(t); |
---|
| 572 | const TableRecord& rec = row.get(0); |
---|
| 573 | Table subt = t( t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 574 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 575 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 576 | ROTableVector<uInt> v(subt, "BEAMNO"); |
---|
[805] | 577 | return int(v.nelements()); |
---|
[105] | 578 | } |
---|
[805] | 579 | return 0; |
---|
| 580 | } |
---|
[455] | 581 | |
---|
[837] | 582 | int Scantable::nif( int scanno ) const |
---|
[805] | 583 | { |
---|
| 584 | if ( scanno < 0 ) { |
---|
| 585 | Int n; |
---|
| 586 | table_.keywordSet().get("nIF",n); |
---|
| 587 | return int(n); |
---|
| 588 | } else { |
---|
| 589 | // take the first POLNO,BEAMNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 590 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 591 | ROTableRow row(t); |
---|
| 592 | const TableRecord& rec = row.get(0); |
---|
| 593 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 594 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 595 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 596 | if ( subt.nrow() == 0 ) return 0; |
---|
| 597 | ROTableVector<uInt> v(subt, "IFNO"); |
---|
[805] | 598 | return int(v.nelements()); |
---|
[2] | 599 | } |
---|
[805] | 600 | return 0; |
---|
| 601 | } |
---|
[321] | 602 | |
---|
[837] | 603 | int Scantable::npol( int scanno ) const |
---|
[805] | 604 | { |
---|
| 605 | if ( scanno < 0 ) { |
---|
| 606 | Int n; |
---|
| 607 | table_.keywordSet().get("nPol",n); |
---|
| 608 | return n; |
---|
| 609 | } else { |
---|
| 610 | // take the first POLNO,IFNO,CYCLENO as nbeam shouldn't vary with these |
---|
[888] | 611 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 612 | ROTableRow row(t); |
---|
| 613 | const TableRecord& rec = row.get(0); |
---|
| 614 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 615 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 616 | && t.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 617 | if ( subt.nrow() == 0 ) return 0; |
---|
| 618 | ROTableVector<uInt> v(subt, "POLNO"); |
---|
[805] | 619 | return int(v.nelements()); |
---|
[321] | 620 | } |
---|
[805] | 621 | return 0; |
---|
[2] | 622 | } |
---|
[805] | 623 | |
---|
[845] | 624 | int Scantable::ncycle( int scanno ) const |
---|
[206] | 625 | { |
---|
[805] | 626 | if ( scanno < 0 ) { |
---|
[837] | 627 | Block<String> cols(2); |
---|
| 628 | cols[0] = "SCANNO"; |
---|
| 629 | cols[1] = "CYCLENO"; |
---|
| 630 | TableIterator it(table_, cols); |
---|
| 631 | int n = 0; |
---|
| 632 | while ( !it.pastEnd() ) { |
---|
| 633 | ++n; |
---|
[902] | 634 | ++it; |
---|
[837] | 635 | } |
---|
| 636 | return n; |
---|
[805] | 637 | } else { |
---|
[888] | 638 | Table t = table_(table_.col("SCANNO") == scanno); |
---|
| 639 | ROTableRow row(t); |
---|
| 640 | const TableRecord& rec = row.get(0); |
---|
| 641 | Table subt = t( t.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 642 | && t.col("POLNO") == Int(rec.asuInt("POLNO")) |
---|
| 643 | && t.col("IFNO") == Int(rec.asuInt("IFNO")) ); |
---|
| 644 | if ( subt.nrow() == 0 ) return 0; |
---|
| 645 | return int(subt.nrow()); |
---|
[805] | 646 | } |
---|
| 647 | return 0; |
---|
[18] | 648 | } |
---|
[455] | 649 | |
---|
| 650 | |
---|
[845] | 651 | int Scantable::nrow( int scanno ) const |
---|
[805] | 652 | { |
---|
[845] | 653 | return int(table_.nrow()); |
---|
| 654 | } |
---|
| 655 | |
---|
| 656 | int Scantable::nchan( int ifno ) const |
---|
| 657 | { |
---|
| 658 | if ( ifno < 0 ) { |
---|
[805] | 659 | Int n; |
---|
| 660 | table_.keywordSet().get("nChan",n); |
---|
| 661 | return int(n); |
---|
| 662 | } else { |
---|
[1360] | 663 | // take the first SCANNO,POLNO,BEAMNO,CYCLENO as nbeam shouldn't |
---|
| 664 | // vary with these |
---|
[2244] | 665 | Table t = table_(table_.col("IFNO") == ifno, 1); |
---|
[888] | 666 | if ( t.nrow() == 0 ) return 0; |
---|
| 667 | ROArrayColumn<Float> v(t, "SPECTRA"); |
---|
[923] | 668 | return v.shape(0)(0); |
---|
[805] | 669 | } |
---|
| 670 | return 0; |
---|
[18] | 671 | } |
---|
[455] | 672 | |
---|
[1111] | 673 | int Scantable::nscan() const { |
---|
| 674 | Vector<uInt> scannos(scanCol_.getColumn()); |
---|
[1148] | 675 | uInt nout = genSort( scannos, Sort::Ascending, |
---|
[1111] | 676 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 677 | return int(nout); |
---|
| 678 | } |
---|
| 679 | |
---|
[923] | 680 | int Scantable::getChannels(int whichrow) const |
---|
| 681 | { |
---|
| 682 | return specCol_.shape(whichrow)(0); |
---|
| 683 | } |
---|
[847] | 684 | |
---|
| 685 | int Scantable::getBeam(int whichrow) const |
---|
| 686 | { |
---|
| 687 | return beamCol_(whichrow); |
---|
| 688 | } |
---|
| 689 | |
---|
[1694] | 690 | std::vector<uint> Scantable::getNumbers(const ScalarColumn<uInt>& col) const |
---|
[1111] | 691 | { |
---|
| 692 | Vector<uInt> nos(col.getColumn()); |
---|
[1148] | 693 | uInt n = genSort( nos, Sort::Ascending, Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 694 | nos.resize(n, True); |
---|
[1111] | 695 | std::vector<uint> stlout; |
---|
| 696 | nos.tovector(stlout); |
---|
| 697 | return stlout; |
---|
| 698 | } |
---|
| 699 | |
---|
[847] | 700 | int Scantable::getIF(int whichrow) const |
---|
| 701 | { |
---|
| 702 | return ifCol_(whichrow); |
---|
| 703 | } |
---|
| 704 | |
---|
| 705 | int Scantable::getPol(int whichrow) const |
---|
| 706 | { |
---|
| 707 | return polCol_(whichrow); |
---|
| 708 | } |
---|
| 709 | |
---|
[805] | 710 | std::string Scantable::formatTime(const MEpoch& me, bool showdate) const |
---|
| 711 | { |
---|
[1947] | 712 | return formatTime(me, showdate, 0); |
---|
| 713 | } |
---|
| 714 | |
---|
| 715 | std::string Scantable::formatTime(const MEpoch& me, bool showdate, uInt prec) const |
---|
| 716 | { |
---|
[805] | 717 | MVTime mvt(me.getValue()); |
---|
| 718 | if (showdate) |
---|
[1947] | 719 | //mvt.setFormat(MVTime::YMD); |
---|
| 720 | mvt.setFormat(MVTime::YMD, prec); |
---|
[805] | 721 | else |
---|
[1947] | 722 | //mvt.setFormat(MVTime::TIME); |
---|
| 723 | mvt.setFormat(MVTime::TIME, prec); |
---|
[805] | 724 | ostringstream oss; |
---|
| 725 | oss << mvt; |
---|
| 726 | return String(oss); |
---|
| 727 | } |
---|
[488] | 728 | |
---|
[805] | 729 | void Scantable::calculateAZEL() |
---|
[2658] | 730 | { |
---|
| 731 | LogIO os( LogOrigin( "Scantable", "calculateAZEL()", WHERE ) ) ; |
---|
[805] | 732 | MPosition mp = getAntennaPosition(); |
---|
| 733 | MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
| 734 | ostringstream oss; |
---|
[2658] | 735 | oss << mp; |
---|
| 736 | os << "Computed azimuth/elevation using " << endl |
---|
| 737 | << String(oss) << endl; |
---|
[996] | 738 | for (Int i=0; i<nrow(); ++i) { |
---|
[805] | 739 | MEpoch me = timeCol(i); |
---|
[987] | 740 | MDirection md = getDirection(i); |
---|
[2658] | 741 | os << " Time: " << formatTime(me,False) |
---|
| 742 | << " Direction: " << formatDirection(md) |
---|
[805] | 743 | << endl << " => "; |
---|
| 744 | MeasFrame frame(mp, me); |
---|
| 745 | Vector<Double> azel = |
---|
| 746 | MDirection::Convert(md, MDirection::Ref(MDirection::AZEL, |
---|
| 747 | frame) |
---|
| 748 | )().getAngle("rad").getValue(); |
---|
[923] | 749 | azCol_.put(i,Float(azel[0])); |
---|
| 750 | elCol_.put(i,Float(azel[1])); |
---|
[2658] | 751 | os << "azel: " << azel[0]/C::pi*180.0 << " " |
---|
| 752 | << azel[1]/C::pi*180.0 << " (deg)" << LogIO::POST; |
---|
[16] | 753 | } |
---|
[805] | 754 | } |
---|
[89] | 755 | |
---|
[1819] | 756 | void Scantable::clip(const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
| 757 | { |
---|
| 758 | for (uInt i=0; i<table_.nrow(); ++i) { |
---|
| 759 | Vector<uChar> flgs = flagsCol_(i); |
---|
| 760 | srchChannelsToClip(i, uthres, dthres, clipoutside, unflag, flgs); |
---|
| 761 | flagsCol_.put(i, flgs); |
---|
| 762 | } |
---|
| 763 | } |
---|
| 764 | |
---|
| 765 | std::vector<bool> Scantable::getClipMask(int whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag) |
---|
| 766 | { |
---|
| 767 | Vector<uChar> flags; |
---|
| 768 | flagsCol_.get(uInt(whichrow), flags); |
---|
| 769 | srchChannelsToClip(uInt(whichrow), uthres, dthres, clipoutside, unflag, flags); |
---|
| 770 | Vector<Bool> bflag(flags.shape()); |
---|
| 771 | convertArray(bflag, flags); |
---|
| 772 | //bflag = !bflag; |
---|
| 773 | |
---|
| 774 | std::vector<bool> mask; |
---|
| 775 | bflag.tovector(mask); |
---|
| 776 | return mask; |
---|
| 777 | } |
---|
| 778 | |
---|
| 779 | void Scantable::srchChannelsToClip(uInt whichrow, const Float uthres, const Float dthres, bool clipoutside, bool unflag, |
---|
| 780 | Vector<uChar> flgs) |
---|
| 781 | { |
---|
| 782 | Vector<Float> spcs = specCol_(whichrow); |
---|
[2348] | 783 | uInt nchannel = spcs.nelements(); |
---|
[1819] | 784 | if (spcs.nelements() != nchannel) { |
---|
| 785 | throw(AipsError("Data has incorrect number of channels")); |
---|
| 786 | } |
---|
| 787 | uChar userflag = 1 << 7; |
---|
| 788 | if (unflag) { |
---|
| 789 | userflag = 0 << 7; |
---|
| 790 | } |
---|
| 791 | if (clipoutside) { |
---|
| 792 | for (uInt j = 0; j < nchannel; ++j) { |
---|
| 793 | Float spc = spcs(j); |
---|
| 794 | if ((spc >= uthres) || (spc <= dthres)) { |
---|
| 795 | flgs(j) = userflag; |
---|
| 796 | } |
---|
| 797 | } |
---|
| 798 | } else { |
---|
| 799 | for (uInt j = 0; j < nchannel; ++j) { |
---|
| 800 | Float spc = spcs(j); |
---|
| 801 | if ((spc < uthres) && (spc > dthres)) { |
---|
| 802 | flgs(j) = userflag; |
---|
| 803 | } |
---|
| 804 | } |
---|
| 805 | } |
---|
| 806 | } |
---|
| 807 | |
---|
[1994] | 808 | |
---|
| 809 | void Scantable::flag( int whichrow, const std::vector<bool>& msk, bool unflag ) { |
---|
[1333] | 810 | std::vector<bool>::const_iterator it; |
---|
| 811 | uInt ntrue = 0; |
---|
[1994] | 812 | if (whichrow >= int(table_.nrow()) ) { |
---|
| 813 | throw(AipsError("Invalid row number")); |
---|
| 814 | } |
---|
[1333] | 815 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
| 816 | if ( *it ) { |
---|
| 817 | ntrue++; |
---|
| 818 | } |
---|
| 819 | } |
---|
[1994] | 820 | //if ( selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
| 821 | if ( whichrow == -1 && !unflag && selector_.empty() && (msk.size() == 0 || msk.size() == ntrue) ) |
---|
[1000] | 822 | throw(AipsError("Trying to flag whole scantable.")); |
---|
[1994] | 823 | uChar userflag = 1 << 7; |
---|
| 824 | if ( unflag ) { |
---|
| 825 | userflag = 0 << 7; |
---|
| 826 | } |
---|
| 827 | if (whichrow > -1 ) { |
---|
| 828 | applyChanFlag(uInt(whichrow), msk, userflag); |
---|
| 829 | } else { |
---|
[1000] | 830 | for ( uInt i=0; i<table_.nrow(); ++i) { |
---|
[1994] | 831 | applyChanFlag(i, msk, userflag); |
---|
[1000] | 832 | } |
---|
[1994] | 833 | } |
---|
| 834 | } |
---|
| 835 | |
---|
| 836 | void Scantable::applyChanFlag( uInt whichrow, const std::vector<bool>& msk, uChar flagval ) |
---|
| 837 | { |
---|
| 838 | if (whichrow >= table_.nrow() ) { |
---|
| 839 | throw( casa::indexError<int>( whichrow, "asap::Scantable::applyChanFlag: Invalid row number" ) ); |
---|
| 840 | } |
---|
| 841 | Vector<uChar> flgs = flagsCol_(whichrow); |
---|
| 842 | if ( msk.size() == 0 ) { |
---|
| 843 | flgs = flagval; |
---|
| 844 | flagsCol_.put(whichrow, flgs); |
---|
[1000] | 845 | return; |
---|
| 846 | } |
---|
[2348] | 847 | if ( int(msk.size()) != nchan( getIF(whichrow) ) ) { |
---|
[1000] | 848 | throw(AipsError("Mask has incorrect number of channels.")); |
---|
| 849 | } |
---|
[1994] | 850 | if ( flgs.nelements() != msk.size() ) { |
---|
| 851 | throw(AipsError("Mask has incorrect number of channels." |
---|
| 852 | " Probably varying with IF. Please flag per IF")); |
---|
| 853 | } |
---|
| 854 | std::vector<bool>::const_iterator it; |
---|
| 855 | uInt j = 0; |
---|
| 856 | for (it = msk.begin(); it != msk.end(); ++it) { |
---|
| 857 | if ( *it ) { |
---|
| 858 | flgs(j) = flagval; |
---|
[1000] | 859 | } |
---|
[1994] | 860 | ++j; |
---|
[1000] | 861 | } |
---|
[1994] | 862 | flagsCol_.put(whichrow, flgs); |
---|
[865] | 863 | } |
---|
| 864 | |
---|
[1819] | 865 | void Scantable::flagRow(const std::vector<uInt>& rows, bool unflag) |
---|
| 866 | { |
---|
[2683] | 867 | if (selector_.empty() && (rows.size() == table_.nrow()) && !unflag) |
---|
[1819] | 868 | throw(AipsError("Trying to flag whole scantable.")); |
---|
| 869 | |
---|
| 870 | uInt rowflag = (unflag ? 0 : 1); |
---|
| 871 | std::vector<uInt>::const_iterator it; |
---|
| 872 | for (it = rows.begin(); it != rows.end(); ++it) |
---|
| 873 | flagrowCol_.put(*it, rowflag); |
---|
| 874 | } |
---|
| 875 | |
---|
[805] | 876 | std::vector<bool> Scantable::getMask(int whichrow) const |
---|
| 877 | { |
---|
| 878 | Vector<uChar> flags; |
---|
| 879 | flagsCol_.get(uInt(whichrow), flags); |
---|
| 880 | Vector<Bool> bflag(flags.shape()); |
---|
| 881 | convertArray(bflag, flags); |
---|
| 882 | bflag = !bflag; |
---|
| 883 | std::vector<bool> mask; |
---|
| 884 | bflag.tovector(mask); |
---|
| 885 | return mask; |
---|
| 886 | } |
---|
[89] | 887 | |
---|
[896] | 888 | std::vector<float> Scantable::getSpectrum( int whichrow, |
---|
[902] | 889 | const std::string& poltype ) const |
---|
[805] | 890 | { |
---|
[2658] | 891 | LogIO os( LogOrigin( "Scantable", "getSpectrum()", WHERE ) ) ; |
---|
| 892 | |
---|
[905] | 893 | String ptype = poltype; |
---|
| 894 | if (poltype == "" ) ptype = getPolType(); |
---|
[902] | 895 | if ( whichrow < 0 || whichrow >= nrow() ) |
---|
| 896 | throw(AipsError("Illegal row number.")); |
---|
[896] | 897 | std::vector<float> out; |
---|
[805] | 898 | Vector<Float> arr; |
---|
[896] | 899 | uInt requestedpol = polCol_(whichrow); |
---|
| 900 | String basetype = getPolType(); |
---|
[905] | 901 | if ( ptype == basetype ) { |
---|
[896] | 902 | specCol_.get(whichrow, arr); |
---|
| 903 | } else { |
---|
[1598] | 904 | CountedPtr<STPol> stpol(STPol::getPolClass(Scantable::factories_, |
---|
[1586] | 905 | basetype)); |
---|
[1334] | 906 | uInt row = uInt(whichrow); |
---|
| 907 | stpol->setSpectra(getPolMatrix(row)); |
---|
[2047] | 908 | Float fang,fhand; |
---|
[1586] | 909 | fang = focusTable_.getTotalAngle(mfocusidCol_(row)); |
---|
[1334] | 910 | fhand = focusTable_.getFeedHand(mfocusidCol_(row)); |
---|
[1586] | 911 | stpol->setPhaseCorrections(fang, fhand); |
---|
[1334] | 912 | arr = stpol->getSpectrum(requestedpol, ptype); |
---|
[896] | 913 | } |
---|
[902] | 914 | if ( arr.nelements() == 0 ) |
---|
[2658] | 915 | |
---|
| 916 | os << "Not enough polarisations present to do the conversion." |
---|
| 917 | << LogIO::POST; |
---|
[805] | 918 | arr.tovector(out); |
---|
| 919 | return out; |
---|
[89] | 920 | } |
---|
[212] | 921 | |
---|
[1360] | 922 | void Scantable::setSpectrum( const std::vector<float>& spec, |
---|
[884] | 923 | int whichrow ) |
---|
| 924 | { |
---|
| 925 | Vector<Float> spectrum(spec); |
---|
| 926 | Vector<Float> arr; |
---|
| 927 | specCol_.get(whichrow, arr); |
---|
| 928 | if ( spectrum.nelements() != arr.nelements() ) |
---|
[896] | 929 | throw AipsError("The spectrum has incorrect number of channels."); |
---|
[884] | 930 | specCol_.put(whichrow, spectrum); |
---|
| 931 | } |
---|
| 932 | |
---|
| 933 | |
---|
[805] | 934 | String Scantable::generateName() |
---|
[745] | 935 | { |
---|
[805] | 936 | return (File::newUniqueName("./","temp")).baseName(); |
---|
[212] | 937 | } |
---|
| 938 | |
---|
[805] | 939 | const casa::Table& Scantable::table( ) const |
---|
[212] | 940 | { |
---|
[805] | 941 | return table_; |
---|
[212] | 942 | } |
---|
| 943 | |
---|
[805] | 944 | casa::Table& Scantable::table( ) |
---|
[386] | 945 | { |
---|
[805] | 946 | return table_; |
---|
[386] | 947 | } |
---|
| 948 | |
---|
[896] | 949 | std::string Scantable::getPolType() const |
---|
| 950 | { |
---|
| 951 | return table_.keywordSet().asString("POLTYPE"); |
---|
| 952 | } |
---|
| 953 | |
---|
[805] | 954 | void Scantable::unsetSelection() |
---|
[380] | 955 | { |
---|
[805] | 956 | table_ = originalTable_; |
---|
[847] | 957 | attach(); |
---|
[805] | 958 | selector_.reset(); |
---|
[380] | 959 | } |
---|
[386] | 960 | |
---|
[805] | 961 | void Scantable::setSelection( const STSelector& selection ) |
---|
[430] | 962 | { |
---|
[805] | 963 | Table tab = const_cast<STSelector&>(selection).apply(originalTable_); |
---|
| 964 | if ( tab.nrow() == 0 ) { |
---|
| 965 | throw(AipsError("Selection contains no data. Not applying it.")); |
---|
| 966 | } |
---|
| 967 | table_ = tab; |
---|
[847] | 968 | attach(); |
---|
[2084] | 969 | // tab.rwKeywordSet().define("nBeam",(Int)(getBeamNos().size())) ; |
---|
| 970 | // vector<uint> selectedIFs = getIFNos() ; |
---|
| 971 | // Int newnIF = selectedIFs.size() ; |
---|
| 972 | // tab.rwKeywordSet().define("nIF",newnIF) ; |
---|
| 973 | // if ( newnIF != 0 ) { |
---|
| 974 | // Int newnChan = 0 ; |
---|
| 975 | // for ( Int i = 0 ; i < newnIF ; i++ ) { |
---|
| 976 | // Int nChan = nchan( selectedIFs[i] ) ; |
---|
| 977 | // if ( newnChan > nChan ) |
---|
| 978 | // newnChan = nChan ; |
---|
| 979 | // } |
---|
| 980 | // tab.rwKeywordSet().define("nChan",newnChan) ; |
---|
| 981 | // } |
---|
| 982 | // tab.rwKeywordSet().define("nPol",(Int)(getPolNos().size())) ; |
---|
[805] | 983 | selector_ = selection; |
---|
[430] | 984 | } |
---|
| 985 | |
---|
[2111] | 986 | |
---|
[2163] | 987 | std::string Scantable::headerSummary() |
---|
[447] | 988 | { |
---|
[805] | 989 | // Format header info |
---|
[2111] | 990 | // STHeader sdh; |
---|
| 991 | // sdh = getHeader(); |
---|
| 992 | // sdh.print(); |
---|
[805] | 993 | ostringstream oss; |
---|
| 994 | oss.flags(std::ios_base::left); |
---|
[2290] | 995 | String tmp; |
---|
| 996 | // Project |
---|
| 997 | table_.keywordSet().get("Project", tmp); |
---|
| 998 | oss << setw(15) << "Project:" << tmp << endl; |
---|
| 999 | // Observation date |
---|
| 1000 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl; |
---|
| 1001 | // Observer |
---|
| 1002 | oss << setw(15) << "Observer:" |
---|
| 1003 | << table_.keywordSet().asString("Observer") << endl; |
---|
| 1004 | // Antenna Name |
---|
| 1005 | table_.keywordSet().get("AntennaName", tmp); |
---|
| 1006 | oss << setw(15) << "Antenna Name:" << tmp << endl; |
---|
| 1007 | // Obs type |
---|
| 1008 | table_.keywordSet().get("Obstype", tmp); |
---|
| 1009 | // Records (nrow) |
---|
| 1010 | oss << setw(15) << "Data Records:" << table_.nrow() << " rows" << endl; |
---|
| 1011 | oss << setw(15) << "Obs. Type:" << tmp << endl; |
---|
| 1012 | // Beams, IFs, Polarizations, and Channels |
---|
[805] | 1013 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl |
---|
| 1014 | << setw(15) << "IFs:" << setw(4) << nif() << endl |
---|
[896] | 1015 | << setw(15) << "Polarisations:" << setw(4) << npol() |
---|
| 1016 | << "(" << getPolType() << ")" << endl |
---|
[1694] | 1017 | << setw(15) << "Channels:" << nchan() << endl; |
---|
[2290] | 1018 | // Flux unit |
---|
| 1019 | table_.keywordSet().get("FluxUnit", tmp); |
---|
| 1020 | oss << setw(15) << "Flux Unit:" << tmp << endl; |
---|
| 1021 | // Abscissa Unit |
---|
| 1022 | oss << setw(15) << "Abscissa:" << getAbcissaLabel(0) << endl; |
---|
| 1023 | // Selection |
---|
| 1024 | oss << selector_.print() << endl; |
---|
| 1025 | |
---|
| 1026 | return String(oss); |
---|
| 1027 | } |
---|
| 1028 | |
---|
| 1029 | void Scantable::summary( const std::string& filename ) |
---|
| 1030 | { |
---|
| 1031 | ostringstream oss; |
---|
| 1032 | ofstream ofs; |
---|
| 1033 | LogIO ols(LogOrigin("Scantable", "summary", WHERE)); |
---|
| 1034 | |
---|
| 1035 | if (filename != "") |
---|
| 1036 | ofs.open( filename.c_str(), ios::out ); |
---|
| 1037 | |
---|
| 1038 | oss << endl; |
---|
| 1039 | oss << asap::SEPERATOR << endl; |
---|
| 1040 | oss << " Scan Table Summary" << endl; |
---|
| 1041 | oss << asap::SEPERATOR << endl; |
---|
| 1042 | |
---|
| 1043 | // Format header info |
---|
| 1044 | oss << headerSummary(); |
---|
| 1045 | oss << endl; |
---|
| 1046 | |
---|
| 1047 | if (table_.nrow() <= 0){ |
---|
| 1048 | oss << asap::SEPERATOR << endl; |
---|
| 1049 | oss << "The MAIN table is empty: there are no data!!!" << endl; |
---|
| 1050 | oss << asap::SEPERATOR << endl; |
---|
| 1051 | |
---|
| 1052 | ols << String(oss) << LogIO::POST; |
---|
| 1053 | if (ofs) { |
---|
| 1054 | ofs << String(oss) << flush; |
---|
| 1055 | ofs.close(); |
---|
| 1056 | } |
---|
| 1057 | return; |
---|
| 1058 | } |
---|
| 1059 | |
---|
| 1060 | |
---|
| 1061 | |
---|
| 1062 | // main table |
---|
| 1063 | String dirtype = "Position (" |
---|
| 1064 | + getDirectionRefString() |
---|
| 1065 | + ")"; |
---|
| 1066 | oss.flags(std::ios_base::left); |
---|
| 1067 | oss << setw(5) << "Scan" |
---|
| 1068 | << setw(15) << "Source" |
---|
| 1069 | << setw(35) << "Time range" |
---|
| 1070 | << setw(2) << "" << setw(7) << "Int[s]" |
---|
| 1071 | << setw(7) << "Record" |
---|
| 1072 | << setw(8) << "SrcType" |
---|
| 1073 | << setw(8) << "FreqIDs" |
---|
| 1074 | << setw(7) << "MolIDs" << endl; |
---|
| 1075 | oss << setw(7)<< "" << setw(6) << "Beam" |
---|
| 1076 | << setw(23) << dirtype << endl; |
---|
| 1077 | |
---|
| 1078 | oss << asap::SEPERATOR << endl; |
---|
| 1079 | |
---|
| 1080 | // Flush summary and clear up the string |
---|
| 1081 | ols << String(oss) << LogIO::POST; |
---|
| 1082 | if (ofs) ofs << String(oss) << flush; |
---|
| 1083 | oss.str(""); |
---|
| 1084 | oss.clear(); |
---|
| 1085 | |
---|
| 1086 | |
---|
| 1087 | // Get Freq_ID map |
---|
| 1088 | ROScalarColumn<uInt> ftabIds(frequencies().table(), "ID"); |
---|
| 1089 | Int nfid = ftabIds.nrow(); |
---|
| 1090 | if (nfid <= 0){ |
---|
| 1091 | oss << "FREQUENCIES subtable is empty: there are no data!!!" << endl; |
---|
| 1092 | oss << asap::SEPERATOR << endl; |
---|
| 1093 | |
---|
| 1094 | ols << String(oss) << LogIO::POST; |
---|
| 1095 | if (ofs) { |
---|
| 1096 | ofs << String(oss) << flush; |
---|
| 1097 | ofs.close(); |
---|
| 1098 | } |
---|
| 1099 | return; |
---|
| 1100 | } |
---|
| 1101 | // Storages of overall IFNO, POLNO, and nchan per FREQ_ID |
---|
| 1102 | // the orders are identical to ID in FREQ subtable |
---|
| 1103 | Block< Vector<uInt> > ifNos(nfid), polNos(nfid); |
---|
| 1104 | Vector<Int> fIdchans(nfid,-1); |
---|
| 1105 | map<uInt, Int> fidMap; // (FREQ_ID, row # in FREQ subtable) pair |
---|
| 1106 | for (Int i=0; i < nfid; i++){ |
---|
| 1107 | // fidMap[freqId] returns row number in FREQ subtable |
---|
| 1108 | fidMap.insert(pair<uInt, Int>(ftabIds(i),i)); |
---|
| 1109 | ifNos[i] = Vector<uInt>(); |
---|
| 1110 | polNos[i] = Vector<uInt>(); |
---|
| 1111 | } |
---|
| 1112 | |
---|
| 1113 | TableIterator iter(table_, "SCANNO"); |
---|
| 1114 | |
---|
| 1115 | // Vars for keeping track of time, freqids, molIds in a SCANNO |
---|
| 1116 | Vector<uInt> freqids; |
---|
| 1117 | Vector<uInt> molids; |
---|
| 1118 | Vector<uInt> beamids(1,0); |
---|
| 1119 | Vector<MDirection> beamDirs; |
---|
| 1120 | Vector<Int> stypeids(1,0); |
---|
| 1121 | Vector<String> stypestrs; |
---|
| 1122 | Int nfreq(1); |
---|
| 1123 | Int nmol(1); |
---|
| 1124 | uInt nbeam(1); |
---|
| 1125 | uInt nstype(1); |
---|
| 1126 | |
---|
| 1127 | Double btime(0.0), etime(0.0); |
---|
| 1128 | Double meanIntTim(0.0); |
---|
| 1129 | |
---|
| 1130 | uInt currFreqId(0), ftabRow(0); |
---|
| 1131 | Int iflen(0), pollen(0); |
---|
| 1132 | |
---|
| 1133 | while (!iter.pastEnd()) { |
---|
| 1134 | Table subt = iter.table(); |
---|
| 1135 | uInt snrow = subt.nrow(); |
---|
| 1136 | ROTableRow row(subt); |
---|
| 1137 | const TableRecord& rec = row.get(0); |
---|
| 1138 | |
---|
| 1139 | // relevant columns |
---|
| 1140 | ROScalarColumn<Double> mjdCol(subt,"TIME"); |
---|
| 1141 | ROScalarColumn<Double> intervalCol(subt,"INTERVAL"); |
---|
| 1142 | MDirection::ROScalarColumn dirCol(subt,"DIRECTION"); |
---|
| 1143 | |
---|
| 1144 | ScalarColumn<uInt> freqIdCol(subt,"FREQ_ID"); |
---|
| 1145 | ScalarColumn<uInt> molIdCol(subt,"MOLECULE_ID"); |
---|
| 1146 | ROScalarColumn<uInt> beamCol(subt,"BEAMNO"); |
---|
| 1147 | ROScalarColumn<Int> stypeCol(subt,"SRCTYPE"); |
---|
| 1148 | |
---|
| 1149 | ROScalarColumn<uInt> ifNoCol(subt,"IFNO"); |
---|
| 1150 | ROScalarColumn<uInt> polNoCol(subt,"POLNO"); |
---|
| 1151 | |
---|
| 1152 | |
---|
| 1153 | // Times |
---|
| 1154 | meanIntTim = sum(intervalCol.getColumn()) / (double) snrow; |
---|
| 1155 | minMax(btime, etime, mjdCol.getColumn()); |
---|
| 1156 | etime += meanIntTim/C::day; |
---|
| 1157 | |
---|
| 1158 | // MOLECULE_ID and FREQ_ID |
---|
| 1159 | molids = getNumbers(molIdCol); |
---|
| 1160 | molids.shape(nmol); |
---|
| 1161 | |
---|
| 1162 | freqids = getNumbers(freqIdCol); |
---|
| 1163 | freqids.shape(nfreq); |
---|
| 1164 | |
---|
| 1165 | // Add first beamid, and srcNames |
---|
| 1166 | beamids.resize(1,False); |
---|
| 1167 | beamDirs.resize(1,False); |
---|
| 1168 | beamids(0)=beamCol(0); |
---|
| 1169 | beamDirs(0)=dirCol(0); |
---|
| 1170 | nbeam = 1; |
---|
| 1171 | |
---|
| 1172 | stypeids.resize(1,False); |
---|
| 1173 | stypeids(0)=stypeCol(0); |
---|
| 1174 | nstype = 1; |
---|
| 1175 | |
---|
| 1176 | // Global listings of nchan/IFNO/POLNO per FREQ_ID |
---|
| 1177 | currFreqId=freqIdCol(0); |
---|
| 1178 | ftabRow = fidMap[currFreqId]; |
---|
| 1179 | // Assumes an identical number of channels per FREQ_ID |
---|
| 1180 | if (fIdchans(ftabRow) < 0 ) { |
---|
| 1181 | RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA"); |
---|
| 1182 | fIdchans(ftabRow)=(*spec).shape()(0); |
---|
| 1183 | } |
---|
| 1184 | // Should keep ifNos and polNos form the previous SCANNO |
---|
| 1185 | if ( !anyEQ(ifNos[ftabRow],ifNoCol(0)) ) { |
---|
| 1186 | ifNos[ftabRow].shape(iflen); |
---|
| 1187 | iflen++; |
---|
| 1188 | ifNos[ftabRow].resize(iflen,True); |
---|
| 1189 | ifNos[ftabRow](iflen-1) = ifNoCol(0); |
---|
| 1190 | } |
---|
| 1191 | if ( !anyEQ(polNos[ftabRow],polNoCol(0)) ) { |
---|
| 1192 | polNos[ftabRow].shape(pollen); |
---|
| 1193 | pollen++; |
---|
| 1194 | polNos[ftabRow].resize(pollen,True); |
---|
| 1195 | polNos[ftabRow](pollen-1) = polNoCol(0); |
---|
| 1196 | } |
---|
| 1197 | |
---|
| 1198 | for (uInt i=1; i < snrow; i++){ |
---|
| 1199 | // Need to list BEAMNO and DIRECTION in the same order |
---|
| 1200 | if ( !anyEQ(beamids,beamCol(i)) ) { |
---|
| 1201 | nbeam++; |
---|
| 1202 | beamids.resize(nbeam,True); |
---|
| 1203 | beamids(nbeam-1)=beamCol(i); |
---|
| 1204 | beamDirs.resize(nbeam,True); |
---|
| 1205 | beamDirs(nbeam-1)=dirCol(i); |
---|
| 1206 | } |
---|
| 1207 | |
---|
| 1208 | // SRCTYPE is Int (getNumber takes only uInt) |
---|
| 1209 | if ( !anyEQ(stypeids,stypeCol(i)) ) { |
---|
| 1210 | nstype++; |
---|
| 1211 | stypeids.resize(nstype,True); |
---|
| 1212 | stypeids(nstype-1)=stypeCol(i); |
---|
| 1213 | } |
---|
| 1214 | |
---|
| 1215 | // Global listings of nchan/IFNO/POLNO per FREQ_ID |
---|
| 1216 | currFreqId=freqIdCol(i); |
---|
| 1217 | ftabRow = fidMap[currFreqId]; |
---|
| 1218 | if (fIdchans(ftabRow) < 0 ) { |
---|
| 1219 | const TableRecord& rec = row.get(i); |
---|
| 1220 | RORecordFieldPtr< Array<Float> > spec(rec, "SPECTRA"); |
---|
| 1221 | fIdchans(ftabRow) = (*spec).shape()(0); |
---|
| 1222 | } |
---|
| 1223 | if ( !anyEQ(ifNos[ftabRow],ifNoCol(i)) ) { |
---|
| 1224 | ifNos[ftabRow].shape(iflen); |
---|
| 1225 | iflen++; |
---|
| 1226 | ifNos[ftabRow].resize(iflen,True); |
---|
| 1227 | ifNos[ftabRow](iflen-1) = ifNoCol(i); |
---|
| 1228 | } |
---|
| 1229 | if ( !anyEQ(polNos[ftabRow],polNoCol(i)) ) { |
---|
| 1230 | polNos[ftabRow].shape(pollen); |
---|
| 1231 | pollen++; |
---|
| 1232 | polNos[ftabRow].resize(pollen,True); |
---|
| 1233 | polNos[ftabRow](pollen-1) = polNoCol(i); |
---|
| 1234 | } |
---|
| 1235 | } // end of row iteration |
---|
| 1236 | |
---|
| 1237 | stypestrs.resize(nstype,False); |
---|
| 1238 | for (uInt j=0; j < nstype; j++) |
---|
| 1239 | stypestrs(j) = SrcType::getName(stypeids(j)); |
---|
| 1240 | |
---|
| 1241 | // Format Scan summary |
---|
| 1242 | oss << setw(4) << std::right << rec.asuInt("SCANNO") |
---|
| 1243 | << std::left << setw(1) << "" |
---|
| 1244 | << setw(15) << rec.asString("SRCNAME") |
---|
| 1245 | << setw(21) << MVTime(btime).string(MVTime::YMD,7) |
---|
| 1246 | << setw(3) << " - " << MVTime(etime).string(MVTime::TIME,7) |
---|
| 1247 | << setw(3) << "" << setw(6) << meanIntTim << setw(1) << "" |
---|
| 1248 | << std::right << setw(5) << snrow << setw(2) << "" |
---|
| 1249 | << std::left << stypestrs << setw(1) << "" |
---|
| 1250 | << freqids << setw(1) << "" |
---|
| 1251 | << molids << endl; |
---|
| 1252 | // Format Beam summary |
---|
| 1253 | for (uInt j=0; j < nbeam; j++) { |
---|
| 1254 | oss << setw(7) << "" << setw(6) << beamids(j) << setw(1) << "" |
---|
| 1255 | << formatDirection(beamDirs(j)) << endl; |
---|
| 1256 | } |
---|
| 1257 | // Flush summary every scan and clear up the string |
---|
| 1258 | ols << String(oss) << LogIO::POST; |
---|
| 1259 | if (ofs) ofs << String(oss) << flush; |
---|
| 1260 | oss.str(""); |
---|
| 1261 | oss.clear(); |
---|
| 1262 | |
---|
| 1263 | ++iter; |
---|
| 1264 | } // end of scan iteration |
---|
| 1265 | oss << asap::SEPERATOR << endl; |
---|
| 1266 | |
---|
| 1267 | // List FRECUENCIES Table (using STFrequencies.print may be slow) |
---|
| 1268 | oss << "FREQUENCIES: " << nfreq << endl; |
---|
| 1269 | oss << std::right << setw(5) << "ID" << setw(2) << "" |
---|
| 1270 | << std::left << setw(5) << "IFNO" << setw(2) << "" |
---|
| 1271 | << setw(8) << "Frame" |
---|
| 1272 | << setw(16) << "RefVal" |
---|
| 1273 | << setw(7) << "RefPix" |
---|
| 1274 | << setw(15) << "Increment" |
---|
| 1275 | << setw(9) << "Channels" |
---|
| 1276 | << setw(6) << "POLNOs" << endl; |
---|
| 1277 | Int tmplen; |
---|
| 1278 | for (Int i=0; i < nfid; i++){ |
---|
| 1279 | // List row=i of FREQUENCIES subtable |
---|
| 1280 | ifNos[i].shape(tmplen); |
---|
[2531] | 1281 | if (tmplen >= 1) { |
---|
[2290] | 1282 | oss << std::right << setw(5) << ftabIds(i) << setw(2) << "" |
---|
| 1283 | << setw(3) << ifNos[i](0) << setw(1) << "" |
---|
| 1284 | << std::left << setw(46) << frequencies().print(ftabIds(i)) |
---|
| 1285 | << setw(2) << "" |
---|
| 1286 | << std::right << setw(8) << fIdchans[i] << setw(2) << "" |
---|
[2531] | 1287 | << std::left << polNos[i]; |
---|
| 1288 | if (tmplen > 1) { |
---|
| 1289 | oss << " (" << tmplen << " chains)"; |
---|
| 1290 | } |
---|
| 1291 | oss << endl; |
---|
[2290] | 1292 | } |
---|
[2531] | 1293 | |
---|
[2290] | 1294 | } |
---|
| 1295 | oss << asap::SEPERATOR << endl; |
---|
| 1296 | |
---|
| 1297 | // List MOLECULES Table (currently lists all rows) |
---|
| 1298 | oss << "MOLECULES: " << endl; |
---|
| 1299 | if (molecules().nrow() <= 0) { |
---|
| 1300 | oss << " MOLECULES subtable is empty: there are no data" << endl; |
---|
| 1301 | } else { |
---|
| 1302 | ROTableRow row(molecules().table()); |
---|
| 1303 | oss << std::right << setw(5) << "ID" |
---|
| 1304 | << std::left << setw(3) << "" |
---|
| 1305 | << setw(18) << "RestFreq" |
---|
| 1306 | << setw(15) << "Name" << endl; |
---|
| 1307 | for (Int i=0; i < molecules().nrow(); i++){ |
---|
| 1308 | const TableRecord& rec=row.get(i); |
---|
| 1309 | oss << std::right << setw(5) << rec.asuInt("ID") |
---|
| 1310 | << std::left << setw(3) << "" |
---|
| 1311 | << rec.asArrayDouble("RESTFREQUENCY") << setw(1) << "" |
---|
| 1312 | << rec.asArrayString("NAME") << endl; |
---|
| 1313 | } |
---|
| 1314 | } |
---|
| 1315 | oss << asap::SEPERATOR << endl; |
---|
| 1316 | ols << String(oss) << LogIO::POST; |
---|
| 1317 | if (ofs) { |
---|
| 1318 | ofs << String(oss) << flush; |
---|
| 1319 | ofs.close(); |
---|
| 1320 | } |
---|
| 1321 | // return String(oss); |
---|
| 1322 | } |
---|
| 1323 | |
---|
| 1324 | |
---|
| 1325 | std::string Scantable::oldheaderSummary() |
---|
| 1326 | { |
---|
| 1327 | // Format header info |
---|
| 1328 | // STHeader sdh; |
---|
| 1329 | // sdh = getHeader(); |
---|
| 1330 | // sdh.print(); |
---|
| 1331 | ostringstream oss; |
---|
| 1332 | oss.flags(std::ios_base::left); |
---|
| 1333 | oss << setw(15) << "Beams:" << setw(4) << nbeam() << endl |
---|
| 1334 | << setw(15) << "IFs:" << setw(4) << nif() << endl |
---|
| 1335 | << setw(15) << "Polarisations:" << setw(4) << npol() |
---|
| 1336 | << "(" << getPolType() << ")" << endl |
---|
| 1337 | << setw(15) << "Channels:" << nchan() << endl; |
---|
[805] | 1338 | String tmp; |
---|
[860] | 1339 | oss << setw(15) << "Observer:" |
---|
| 1340 | << table_.keywordSet().asString("Observer") << endl; |
---|
[805] | 1341 | oss << setw(15) << "Obs Date:" << getTime(-1,true) << endl; |
---|
| 1342 | table_.keywordSet().get("Project", tmp); |
---|
| 1343 | oss << setw(15) << "Project:" << tmp << endl; |
---|
| 1344 | table_.keywordSet().get("Obstype", tmp); |
---|
| 1345 | oss << setw(15) << "Obs. Type:" << tmp << endl; |
---|
| 1346 | table_.keywordSet().get("AntennaName", tmp); |
---|
| 1347 | oss << setw(15) << "Antenna Name:" << tmp << endl; |
---|
| 1348 | table_.keywordSet().get("FluxUnit", tmp); |
---|
| 1349 | oss << setw(15) << "Flux Unit:" << tmp << endl; |
---|
[1819] | 1350 | int nid = moleculeTable_.nrow(); |
---|
| 1351 | Bool firstline = True; |
---|
[805] | 1352 | oss << setw(15) << "Rest Freqs:"; |
---|
[1819] | 1353 | for (int i=0; i<nid; i++) { |
---|
[2244] | 1354 | Table t = table_(table_.col("MOLECULE_ID") == i, 1); |
---|
[1819] | 1355 | if (t.nrow() > 0) { |
---|
| 1356 | Vector<Double> vec(moleculeTable_.getRestFrequency(i)); |
---|
| 1357 | if (vec.nelements() > 0) { |
---|
| 1358 | if (firstline) { |
---|
| 1359 | oss << setprecision(10) << vec << " [Hz]" << endl; |
---|
| 1360 | firstline=False; |
---|
| 1361 | } |
---|
| 1362 | else{ |
---|
| 1363 | oss << setw(15)<<" " << setprecision(10) << vec << " [Hz]" << endl; |
---|
| 1364 | } |
---|
| 1365 | } else { |
---|
| 1366 | oss << "none" << endl; |
---|
| 1367 | } |
---|
| 1368 | } |
---|
[805] | 1369 | } |
---|
[941] | 1370 | |
---|
| 1371 | oss << setw(15) << "Abcissa:" << getAbcissaLabel(0) << endl; |
---|
[805] | 1372 | oss << selector_.print() << endl; |
---|
[2111] | 1373 | return String(oss); |
---|
| 1374 | } |
---|
| 1375 | |
---|
[2286] | 1376 | //std::string Scantable::summary( const std::string& filename ) |
---|
[2290] | 1377 | void Scantable::oldsummary( const std::string& filename ) |
---|
[2111] | 1378 | { |
---|
| 1379 | ostringstream oss; |
---|
[2286] | 1380 | ofstream ofs; |
---|
| 1381 | LogIO ols(LogOrigin("Scantable", "summary", WHERE)); |
---|
| 1382 | |
---|
| 1383 | if (filename != "") |
---|
| 1384 | ofs.open( filename.c_str(), ios::out ); |
---|
| 1385 | |
---|
[805] | 1386 | oss << endl; |
---|
[2111] | 1387 | oss << asap::SEPERATOR << endl; |
---|
| 1388 | oss << " Scan Table Summary" << endl; |
---|
| 1389 | oss << asap::SEPERATOR << endl; |
---|
| 1390 | |
---|
| 1391 | // Format header info |
---|
[2290] | 1392 | oss << oldheaderSummary(); |
---|
[2111] | 1393 | oss << endl; |
---|
| 1394 | |
---|
[805] | 1395 | // main table |
---|
| 1396 | String dirtype = "Position (" |
---|
[987] | 1397 | + getDirectionRefString() |
---|
[805] | 1398 | + ")"; |
---|
[2111] | 1399 | oss.flags(std::ios_base::left); |
---|
[941] | 1400 | oss << setw(5) << "Scan" << setw(15) << "Source" |
---|
[2005] | 1401 | << setw(10) << "Time" << setw(18) << "Integration" |
---|
| 1402 | << setw(15) << "Source Type" << endl; |
---|
[941] | 1403 | oss << setw(5) << "" << setw(5) << "Beam" << setw(3) << "" << dirtype << endl; |
---|
[1694] | 1404 | oss << setw(10) << "" << setw(3) << "IF" << setw(3) << "" |
---|
[805] | 1405 | << setw(8) << "Frame" << setw(16) |
---|
[1694] | 1406 | << "RefVal" << setw(10) << "RefPix" << setw(12) << "Increment" |
---|
| 1407 | << setw(7) << "Channels" |
---|
| 1408 | << endl; |
---|
[805] | 1409 | oss << asap::SEPERATOR << endl; |
---|
[2286] | 1410 | |
---|
| 1411 | // Flush summary and clear up the string |
---|
| 1412 | ols << String(oss) << LogIO::POST; |
---|
| 1413 | if (ofs) ofs << String(oss) << flush; |
---|
| 1414 | oss.str(""); |
---|
| 1415 | oss.clear(); |
---|
| 1416 | |
---|
[805] | 1417 | TableIterator iter(table_, "SCANNO"); |
---|
| 1418 | while (!iter.pastEnd()) { |
---|
| 1419 | Table subt = iter.table(); |
---|
| 1420 | ROTableRow row(subt); |
---|
| 1421 | MEpoch::ROScalarColumn timeCol(subt,"TIME"); |
---|
| 1422 | const TableRecord& rec = row.get(0); |
---|
| 1423 | oss << setw(4) << std::right << rec.asuInt("SCANNO") |
---|
| 1424 | << std::left << setw(1) << "" |
---|
| 1425 | << setw(15) << rec.asString("SRCNAME") |
---|
| 1426 | << setw(10) << formatTime(timeCol(0), false); |
---|
| 1427 | // count the cycles in the scan |
---|
| 1428 | TableIterator cyciter(subt, "CYCLENO"); |
---|
| 1429 | int nint = 0; |
---|
| 1430 | while (!cyciter.pastEnd()) { |
---|
| 1431 | ++nint; |
---|
| 1432 | ++cyciter; |
---|
| 1433 | } |
---|
| 1434 | oss << setw(3) << std::right << nint << setw(3) << " x " << std::left |
---|
[2005] | 1435 | << setw(11) << formatSec(rec.asFloat("INTERVAL")) << setw(1) << "" |
---|
| 1436 | << setw(15) << SrcType::getName(rec.asInt("SRCTYPE")) << endl; |
---|
[447] | 1437 | |
---|
[805] | 1438 | TableIterator biter(subt, "BEAMNO"); |
---|
| 1439 | while (!biter.pastEnd()) { |
---|
| 1440 | Table bsubt = biter.table(); |
---|
| 1441 | ROTableRow brow(bsubt); |
---|
| 1442 | const TableRecord& brec = brow.get(0); |
---|
[1000] | 1443 | uInt row0 = bsubt.rowNumbers(table_)[0]; |
---|
[941] | 1444 | oss << setw(5) << "" << setw(4) << std::right << brec.asuInt("BEAMNO")<< std::left; |
---|
[987] | 1445 | oss << setw(4) << "" << formatDirection(getDirection(row0)) << endl; |
---|
[805] | 1446 | TableIterator iiter(bsubt, "IFNO"); |
---|
| 1447 | while (!iiter.pastEnd()) { |
---|
| 1448 | Table isubt = iiter.table(); |
---|
| 1449 | ROTableRow irow(isubt); |
---|
| 1450 | const TableRecord& irec = irow.get(0); |
---|
[1694] | 1451 | oss << setw(9) << ""; |
---|
[941] | 1452 | oss << setw(3) << std::right << irec.asuInt("IFNO") << std::left |
---|
[1694] | 1453 | << setw(1) << "" << frequencies().print(irec.asuInt("FREQ_ID")) |
---|
| 1454 | << setw(3) << "" << nchan(irec.asuInt("IFNO")) |
---|
[1375] | 1455 | << endl; |
---|
[447] | 1456 | |
---|
[805] | 1457 | ++iiter; |
---|
| 1458 | } |
---|
| 1459 | ++biter; |
---|
| 1460 | } |
---|
[2286] | 1461 | // Flush summary every scan and clear up the string |
---|
| 1462 | ols << String(oss) << LogIO::POST; |
---|
| 1463 | if (ofs) ofs << String(oss) << flush; |
---|
| 1464 | oss.str(""); |
---|
| 1465 | oss.clear(); |
---|
| 1466 | |
---|
[805] | 1467 | ++iter; |
---|
[447] | 1468 | } |
---|
[2286] | 1469 | oss << asap::SEPERATOR << endl; |
---|
| 1470 | ols << String(oss) << LogIO::POST; |
---|
| 1471 | if (ofs) { |
---|
[2290] | 1472 | ofs << String(oss) << flush; |
---|
[2286] | 1473 | ofs.close(); |
---|
| 1474 | } |
---|
| 1475 | // return String(oss); |
---|
[447] | 1476 | } |
---|
| 1477 | |
---|
[1947] | 1478 | // std::string Scantable::getTime(int whichrow, bool showdate) const |
---|
| 1479 | // { |
---|
| 1480 | // MEpoch::ROScalarColumn timeCol(table_, "TIME"); |
---|
| 1481 | // MEpoch me; |
---|
| 1482 | // if (whichrow > -1) { |
---|
| 1483 | // me = timeCol(uInt(whichrow)); |
---|
| 1484 | // } else { |
---|
| 1485 | // Double tm; |
---|
| 1486 | // table_.keywordSet().get("UTC",tm); |
---|
| 1487 | // me = MEpoch(MVEpoch(tm)); |
---|
| 1488 | // } |
---|
| 1489 | // return formatTime(me, showdate); |
---|
| 1490 | // } |
---|
| 1491 | |
---|
| 1492 | std::string Scantable::getTime(int whichrow, bool showdate, uInt prec) const |
---|
[777] | 1493 | { |
---|
[805] | 1494 | MEpoch me; |
---|
[1947] | 1495 | me = getEpoch(whichrow); |
---|
| 1496 | return formatTime(me, showdate, prec); |
---|
[777] | 1497 | } |
---|
[805] | 1498 | |
---|
[1411] | 1499 | MEpoch Scantable::getEpoch(int whichrow) const |
---|
| 1500 | { |
---|
| 1501 | if (whichrow > -1) { |
---|
| 1502 | return timeCol_(uInt(whichrow)); |
---|
| 1503 | } else { |
---|
| 1504 | Double tm; |
---|
| 1505 | table_.keywordSet().get("UTC",tm); |
---|
[1598] | 1506 | return MEpoch(MVEpoch(tm)); |
---|
[1411] | 1507 | } |
---|
| 1508 | } |
---|
| 1509 | |
---|
[1068] | 1510 | std::string Scantable::getDirectionString(int whichrow) const |
---|
| 1511 | { |
---|
| 1512 | return formatDirection(getDirection(uInt(whichrow))); |
---|
| 1513 | } |
---|
| 1514 | |
---|
[1598] | 1515 | |
---|
| 1516 | SpectralCoordinate Scantable::getSpectralCoordinate(int whichrow) const { |
---|
| 1517 | const MPosition& mp = getAntennaPosition(); |
---|
| 1518 | const MDirection& md = getDirection(whichrow); |
---|
| 1519 | const MEpoch& me = timeCol_(whichrow); |
---|
[1819] | 1520 | //Double rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
| 1521 | Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
[2346] | 1522 | return freqTable_.getSpectralCoordinate(md, mp, me, rf, |
---|
[1598] | 1523 | mfreqidCol_(whichrow)); |
---|
| 1524 | } |
---|
| 1525 | |
---|
[1360] | 1526 | std::vector< double > Scantable::getAbcissa( int whichrow ) const |
---|
[865] | 1527 | { |
---|
[1507] | 1528 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal row number")); |
---|
[865] | 1529 | std::vector<double> stlout; |
---|
| 1530 | int nchan = specCol_(whichrow).nelements(); |
---|
[2346] | 1531 | String us = freqTable_.getUnitString(); |
---|
[865] | 1532 | if ( us == "" || us == "pixel" || us == "channel" ) { |
---|
| 1533 | for (int i=0; i<nchan; ++i) { |
---|
| 1534 | stlout.push_back(double(i)); |
---|
| 1535 | } |
---|
| 1536 | return stlout; |
---|
| 1537 | } |
---|
[1598] | 1538 | SpectralCoordinate spc = getSpectralCoordinate(whichrow); |
---|
[865] | 1539 | Vector<Double> pixel(nchan); |
---|
| 1540 | Vector<Double> world; |
---|
| 1541 | indgen(pixel); |
---|
| 1542 | if ( Unit(us) == Unit("Hz") ) { |
---|
| 1543 | for ( int i=0; i < nchan; ++i) { |
---|
| 1544 | Double world; |
---|
| 1545 | spc.toWorld(world, pixel[i]); |
---|
| 1546 | stlout.push_back(double(world)); |
---|
| 1547 | } |
---|
| 1548 | } else if ( Unit(us) == Unit("km/s") ) { |
---|
| 1549 | Vector<Double> world; |
---|
| 1550 | spc.pixelToVelocity(world, pixel); |
---|
| 1551 | world.tovector(stlout); |
---|
| 1552 | } |
---|
| 1553 | return stlout; |
---|
| 1554 | } |
---|
[1360] | 1555 | void Scantable::setDirectionRefString( const std::string & refstr ) |
---|
[987] | 1556 | { |
---|
| 1557 | MDirection::Types mdt; |
---|
| 1558 | if (refstr != "" && !MDirection::getType(mdt, refstr)) { |
---|
| 1559 | throw(AipsError("Illegal Direction frame.")); |
---|
| 1560 | } |
---|
| 1561 | if ( refstr == "" ) { |
---|
| 1562 | String defaultstr = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
| 1563 | table_.rwKeywordSet().define("DIRECTIONREF", defaultstr); |
---|
| 1564 | } else { |
---|
| 1565 | table_.rwKeywordSet().define("DIRECTIONREF", String(refstr)); |
---|
| 1566 | } |
---|
| 1567 | } |
---|
[865] | 1568 | |
---|
[1360] | 1569 | std::string Scantable::getDirectionRefString( ) const |
---|
[987] | 1570 | { |
---|
| 1571 | return table_.keywordSet().asString("DIRECTIONREF"); |
---|
| 1572 | } |
---|
| 1573 | |
---|
| 1574 | MDirection Scantable::getDirection(int whichrow ) const |
---|
| 1575 | { |
---|
| 1576 | String usertype = table_.keywordSet().asString("DIRECTIONREF"); |
---|
| 1577 | String type = MDirection::showType(dirCol_.getMeasRef().getType()); |
---|
| 1578 | if ( usertype != type ) { |
---|
| 1579 | MDirection::Types mdt; |
---|
| 1580 | if (!MDirection::getType(mdt, usertype)) { |
---|
| 1581 | throw(AipsError("Illegal Direction frame.")); |
---|
| 1582 | } |
---|
| 1583 | return dirCol_.convert(uInt(whichrow), mdt); |
---|
| 1584 | } else { |
---|
| 1585 | return dirCol_(uInt(whichrow)); |
---|
| 1586 | } |
---|
| 1587 | } |
---|
| 1588 | |
---|
[847] | 1589 | std::string Scantable::getAbcissaLabel( int whichrow ) const |
---|
| 1590 | { |
---|
[996] | 1591 | if ( whichrow > int(table_.nrow()) ) throw(AipsError("Illegal ro number")); |
---|
[847] | 1592 | const MPosition& mp = getAntennaPosition(); |
---|
[987] | 1593 | const MDirection& md = getDirection(whichrow); |
---|
[847] | 1594 | const MEpoch& me = timeCol_(whichrow); |
---|
[1819] | 1595 | //const Double& rf = mmolidCol_(whichrow); |
---|
| 1596 | const Vector<Double> rf = moleculeTable_.getRestFrequency(mmolidCol_(whichrow)); |
---|
[847] | 1597 | SpectralCoordinate spc = |
---|
[2346] | 1598 | freqTable_.getSpectralCoordinate(md, mp, me, rf, mfreqidCol_(whichrow)); |
---|
[847] | 1599 | |
---|
| 1600 | String s = "Channel"; |
---|
[2346] | 1601 | Unit u = Unit(freqTable_.getUnitString()); |
---|
[847] | 1602 | if (u == Unit("km/s")) { |
---|
[1170] | 1603 | s = CoordinateUtil::axisLabel(spc, 0, True,True, True); |
---|
[847] | 1604 | } else if (u == Unit("Hz")) { |
---|
| 1605 | Vector<String> wau(1);wau = u.getName(); |
---|
| 1606 | spc.setWorldAxisUnits(wau); |
---|
[1170] | 1607 | s = CoordinateUtil::axisLabel(spc, 0, True, True, False); |
---|
[847] | 1608 | } |
---|
| 1609 | return s; |
---|
| 1610 | |
---|
| 1611 | } |
---|
| 1612 | |
---|
[1819] | 1613 | /** |
---|
| 1614 | void asap::Scantable::setRestFrequencies( double rf, const std::string& name, |
---|
[1170] | 1615 | const std::string& unit ) |
---|
[1819] | 1616 | **/ |
---|
| 1617 | void Scantable::setRestFrequencies( vector<double> rf, const vector<std::string>& name, |
---|
| 1618 | const std::string& unit ) |
---|
| 1619 | |
---|
[847] | 1620 | { |
---|
[923] | 1621 | ///@todo lookup in line table to fill in name and formattedname |
---|
[847] | 1622 | Unit u(unit); |
---|
[1819] | 1623 | //Quantum<Double> urf(rf, u); |
---|
| 1624 | Quantum<Vector<Double> >urf(rf, u); |
---|
| 1625 | Vector<String> formattedname(0); |
---|
| 1626 | //cerr<<"Scantable::setRestFrequnecies="<<urf<<endl; |
---|
| 1627 | |
---|
| 1628 | //uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), name, ""); |
---|
| 1629 | uInt id = moleculeTable_.addEntry(urf.getValue("Hz"), mathutil::toVectorString(name), formattedname); |
---|
[847] | 1630 | TableVector<uInt> tabvec(table_, "MOLECULE_ID"); |
---|
| 1631 | tabvec = id; |
---|
| 1632 | } |
---|
| 1633 | |
---|
[1819] | 1634 | /** |
---|
| 1635 | void asap::Scantable::setRestFrequencies( const std::string& name ) |
---|
[847] | 1636 | { |
---|
| 1637 | throw(AipsError("setRestFrequencies( const std::string& name ) NYI")); |
---|
| 1638 | ///@todo implement |
---|
| 1639 | } |
---|
[1819] | 1640 | **/ |
---|
[2012] | 1641 | |
---|
[1819] | 1642 | void Scantable::setRestFrequencies( const vector<std::string>& name ) |
---|
| 1643 | { |
---|
[2163] | 1644 | (void) name; // suppress unused warning |
---|
[1819] | 1645 | throw(AipsError("setRestFrequencies( const vector<std::string>& name ) NYI")); |
---|
| 1646 | ///@todo implement |
---|
| 1647 | } |
---|
[847] | 1648 | |
---|
[1360] | 1649 | std::vector< unsigned int > Scantable::rownumbers( ) const |
---|
[852] | 1650 | { |
---|
| 1651 | std::vector<unsigned int> stlout; |
---|
| 1652 | Vector<uInt> vec = table_.rowNumbers(); |
---|
| 1653 | vec.tovector(stlout); |
---|
| 1654 | return stlout; |
---|
| 1655 | } |
---|
| 1656 | |
---|
[865] | 1657 | |
---|
[1360] | 1658 | Matrix<Float> Scantable::getPolMatrix( uInt whichrow ) const |
---|
[896] | 1659 | { |
---|
| 1660 | ROTableRow row(table_); |
---|
| 1661 | const TableRecord& rec = row.get(whichrow); |
---|
| 1662 | Table t = |
---|
| 1663 | originalTable_( originalTable_.col("SCANNO") == Int(rec.asuInt("SCANNO")) |
---|
| 1664 | && originalTable_.col("BEAMNO") == Int(rec.asuInt("BEAMNO")) |
---|
| 1665 | && originalTable_.col("IFNO") == Int(rec.asuInt("IFNO")) |
---|
| 1666 | && originalTable_.col("CYCLENO") == Int(rec.asuInt("CYCLENO")) ); |
---|
| 1667 | ROArrayColumn<Float> speccol(t, "SPECTRA"); |
---|
| 1668 | return speccol.getColumn(); |
---|
| 1669 | } |
---|
[865] | 1670 | |
---|
[1360] | 1671 | std::vector< std::string > Scantable::columnNames( ) const |
---|
[902] | 1672 | { |
---|
| 1673 | Vector<String> vec = table_.tableDesc().columnNames(); |
---|
| 1674 | return mathutil::tovectorstring(vec); |
---|
| 1675 | } |
---|
[896] | 1676 | |
---|
[1360] | 1677 | MEpoch::Types Scantable::getTimeReference( ) const |
---|
[915] | 1678 | { |
---|
| 1679 | return MEpoch::castType(timeCol_.getMeasRef().getType()); |
---|
[972] | 1680 | } |
---|
[915] | 1681 | |
---|
[1360] | 1682 | void Scantable::addFit( const STFitEntry& fit, int row ) |
---|
[972] | 1683 | { |
---|
[1819] | 1684 | //cout << mfitidCol_(uInt(row)) << endl; |
---|
| 1685 | LogIO os( LogOrigin( "Scantable", "addFit()", WHERE ) ) ; |
---|
| 1686 | os << mfitidCol_(uInt(row)) << LogIO::POST ; |
---|
[972] | 1687 | uInt id = fitTable_.addEntry(fit, mfitidCol_(uInt(row))); |
---|
| 1688 | mfitidCol_.put(uInt(row), id); |
---|
| 1689 | } |
---|
[915] | 1690 | |
---|
[1360] | 1691 | void Scantable::shift(int npix) |
---|
| 1692 | { |
---|
| 1693 | Vector<uInt> fids(mfreqidCol_.getColumn()); |
---|
| 1694 | genSort( fids, Sort::Ascending, |
---|
| 1695 | Sort::QuickSort|Sort::NoDuplicates ); |
---|
| 1696 | for (uInt i=0; i<fids.nelements(); ++i) { |
---|
[1567] | 1697 | frequencies().shiftRefPix(npix, fids[i]); |
---|
[1360] | 1698 | } |
---|
| 1699 | } |
---|
[987] | 1700 | |
---|
[1819] | 1701 | String Scantable::getAntennaName() const |
---|
[1391] | 1702 | { |
---|
| 1703 | String out; |
---|
| 1704 | table_.keywordSet().get("AntennaName", out); |
---|
[1987] | 1705 | String::size_type pos1 = out.find("@") ; |
---|
| 1706 | String::size_type pos2 = out.find("//") ; |
---|
| 1707 | if ( pos2 != String::npos ) |
---|
[2036] | 1708 | out = out.substr(pos2+2,pos1-pos2-2) ; |
---|
[1987] | 1709 | else if ( pos1 != String::npos ) |
---|
| 1710 | out = out.substr(0,pos1) ; |
---|
[1391] | 1711 | return out; |
---|
[987] | 1712 | } |
---|
[1391] | 1713 | |
---|
[1730] | 1714 | int Scantable::checkScanInfo(const std::vector<int>& scanlist) const |
---|
[1391] | 1715 | { |
---|
| 1716 | String tbpath; |
---|
| 1717 | int ret = 0; |
---|
| 1718 | if ( table_.keywordSet().isDefined("GBT_GO") ) { |
---|
| 1719 | table_.keywordSet().get("GBT_GO", tbpath); |
---|
| 1720 | Table t(tbpath,Table::Old); |
---|
| 1721 | // check each scan if other scan of the pair exist |
---|
| 1722 | int nscan = scanlist.size(); |
---|
| 1723 | for (int i = 0; i < nscan; i++) { |
---|
| 1724 | Table subt = t( t.col("SCAN") == scanlist[i]+1 ); |
---|
| 1725 | if (subt.nrow()==0) { |
---|
[1819] | 1726 | //cerr <<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<endl; |
---|
| 1727 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1728 | os <<LogIO::WARN<<"Scan "<<scanlist[i]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
[1391] | 1729 | ret = 1; |
---|
| 1730 | break; |
---|
| 1731 | } |
---|
| 1732 | ROTableRow row(subt); |
---|
| 1733 | const TableRecord& rec = row.get(0); |
---|
| 1734 | int scan1seqn = rec.asuInt("PROCSEQN"); |
---|
| 1735 | int laston1 = rec.asuInt("LASTON"); |
---|
| 1736 | if ( rec.asuInt("PROCSIZE")==2 ) { |
---|
| 1737 | if ( i < nscan-1 ) { |
---|
| 1738 | Table subt2 = t( t.col("SCAN") == scanlist[i+1]+1 ); |
---|
| 1739 | if ( subt2.nrow() == 0) { |
---|
[1819] | 1740 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1741 | |
---|
| 1742 | //cerr<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<endl; |
---|
| 1743 | os<<LogIO::WARN<<"Scan "<<scanlist[i+1]<<" cannot be found in the scantable."<<LogIO::POST; |
---|
[1391] | 1744 | ret = 1; |
---|
| 1745 | break; |
---|
| 1746 | } |
---|
| 1747 | ROTableRow row2(subt2); |
---|
| 1748 | const TableRecord& rec2 = row2.get(0); |
---|
| 1749 | int scan2seqn = rec2.asuInt("PROCSEQN"); |
---|
| 1750 | int laston2 = rec2.asuInt("LASTON"); |
---|
| 1751 | if (scan1seqn == 1 && scan2seqn == 2) { |
---|
| 1752 | if (laston1 == laston2) { |
---|
[1819] | 1753 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1754 | //cerr<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
| 1755 | os<<"A valid scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
[1391] | 1756 | i +=1; |
---|
| 1757 | } |
---|
| 1758 | else { |
---|
[1819] | 1759 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1760 | //cerr<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<endl; |
---|
| 1761 | os<<LogIO::WARN<<"Incorrect scan pair ["<<scanlist[i]<<","<<scanlist[i+1]<<"]"<<LogIO::POST; |
---|
[1391] | 1762 | } |
---|
| 1763 | } |
---|
| 1764 | else if (scan1seqn==2 && scan2seqn == 1) { |
---|
| 1765 | if (laston1 == laston2) { |
---|
[1819] | 1766 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1767 | //cerr<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<endl; |
---|
| 1768 | os<<LogIO::WARN<<"["<<scanlist[i]<<","<<scanlist[i+1]<<"] is a valid scan pair but in incorrect order."<<LogIO::POST; |
---|
[1391] | 1769 | ret = 1; |
---|
| 1770 | break; |
---|
| 1771 | } |
---|
| 1772 | } |
---|
| 1773 | else { |
---|
[1819] | 1774 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1775 | //cerr<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<endl; |
---|
| 1776 | os<<LogIO::WARN<<"The other scan for "<<scanlist[i]<<" appears to be missing. Check the input scan numbers."<<LogIO::POST; |
---|
[1391] | 1777 | ret = 1; |
---|
| 1778 | break; |
---|
| 1779 | } |
---|
| 1780 | } |
---|
| 1781 | } |
---|
| 1782 | else { |
---|
[1819] | 1783 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1784 | //cerr<<"The scan does not appear to be standard obsevation."<<endl; |
---|
| 1785 | os<<LogIO::WARN<<"The scan does not appear to be standard obsevation."<<LogIO::POST; |
---|
[1391] | 1786 | } |
---|
| 1787 | //if ( i >= nscan ) break; |
---|
| 1788 | } |
---|
| 1789 | } |
---|
| 1790 | else { |
---|
[1819] | 1791 | LogIO os( LogOrigin( "Scantable", "checkScanInfo()", WHERE ) ) ; |
---|
| 1792 | //cerr<<"No reference to GBT_GO table."<<endl; |
---|
| 1793 | os<<LogIO::WARN<<"No reference to GBT_GO table."<<LogIO::POST; |
---|
[1391] | 1794 | ret = 1; |
---|
| 1795 | } |
---|
| 1796 | return ret; |
---|
| 1797 | } |
---|
| 1798 | |
---|
[1730] | 1799 | std::vector<double> Scantable::getDirectionVector(int whichrow) const |
---|
[1391] | 1800 | { |
---|
| 1801 | Vector<Double> Dir = dirCol_(whichrow).getAngle("rad").getValue(); |
---|
| 1802 | std::vector<double> dir; |
---|
| 1803 | Dir.tovector(dir); |
---|
| 1804 | return dir; |
---|
| 1805 | } |
---|
| 1806 | |
---|
[1819] | 1807 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax ) |
---|
| 1808 | throw( casa::AipsError ) |
---|
| 1809 | { |
---|
| 1810 | // assumed that all rows have same nChan |
---|
| 1811 | Vector<Float> arr = specCol_( 0 ) ; |
---|
| 1812 | int nChan = arr.nelements() ; |
---|
| 1813 | |
---|
| 1814 | // if nmin < 0 or nmax < 0, nothing to do |
---|
| 1815 | if ( nmin < 0 ) { |
---|
| 1816 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
| 1817 | } |
---|
| 1818 | if ( nmax < 0 ) { |
---|
| 1819 | throw( casa::indexError<int>( nmax, "asap::Scantable::reshapeSpectrum: Invalid range. Negative index is specified." ) ) ; |
---|
| 1820 | } |
---|
| 1821 | |
---|
| 1822 | // if nmin > nmax, exchange values |
---|
| 1823 | if ( nmin > nmax ) { |
---|
| 1824 | int tmp = nmax ; |
---|
| 1825 | nmax = nmin ; |
---|
| 1826 | nmin = tmp ; |
---|
| 1827 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1828 | os << "Swap values. Applied range is [" |
---|
| 1829 | << nmin << ", " << nmax << "]" << LogIO::POST ; |
---|
| 1830 | } |
---|
| 1831 | |
---|
| 1832 | // if nmin exceeds nChan, nothing to do |
---|
| 1833 | if ( nmin >= nChan ) { |
---|
| 1834 | throw( casa::indexError<int>( nmin, "asap::Scantable::reshapeSpectrum: Invalid range. Specified minimum exceeds nChan." ) ) ; |
---|
| 1835 | } |
---|
| 1836 | |
---|
| 1837 | // if nmax exceeds nChan, reset nmax to nChan |
---|
[2672] | 1838 | if ( nmax >= nChan-1 ) { |
---|
[1819] | 1839 | if ( nmin == 0 ) { |
---|
| 1840 | // nothing to do |
---|
| 1841 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1842 | os << "Whole range is selected. Nothing to do." << LogIO::POST ; |
---|
| 1843 | return ; |
---|
| 1844 | } |
---|
| 1845 | else { |
---|
| 1846 | LogIO os( LogOrigin( "Scantable", "reshapeSpectrum()", WHERE ) ) ; |
---|
| 1847 | os << "Specified maximum exceeds nChan. Applied range is [" |
---|
| 1848 | << nmin << ", " << nChan-1 << "]." << LogIO::POST ; |
---|
| 1849 | nmax = nChan - 1 ; |
---|
| 1850 | } |
---|
| 1851 | } |
---|
| 1852 | |
---|
| 1853 | // reshape specCol_ and flagCol_ |
---|
| 1854 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
| 1855 | reshapeSpectrum( nmin, nmax, irow ) ; |
---|
| 1856 | } |
---|
| 1857 | |
---|
| 1858 | // update FREQUENCIES subtable |
---|
| 1859 | Double refpix ; |
---|
| 1860 | Double refval ; |
---|
| 1861 | Double increment ; |
---|
[2346] | 1862 | int freqnrow = freqTable_.table().nrow() ; |
---|
[1819] | 1863 | Vector<uInt> oldId( freqnrow ) ; |
---|
| 1864 | Vector<uInt> newId( freqnrow ) ; |
---|
| 1865 | for ( int irow = 0 ; irow < freqnrow ; irow++ ) { |
---|
[2346] | 1866 | freqTable_.getEntry( refpix, refval, increment, irow ) ; |
---|
[1819] | 1867 | /*** |
---|
| 1868 | * need to shift refpix to nmin |
---|
| 1869 | * note that channel nmin in old index will be channel 0 in new one |
---|
| 1870 | ***/ |
---|
| 1871 | refval = refval - ( refpix - nmin ) * increment ; |
---|
| 1872 | refpix = 0 ; |
---|
[2346] | 1873 | freqTable_.setEntry( refpix, refval, increment, irow ) ; |
---|
[1819] | 1874 | } |
---|
| 1875 | |
---|
| 1876 | // update nchan |
---|
| 1877 | int newsize = nmax - nmin + 1 ; |
---|
| 1878 | table_.rwKeywordSet().define( "nChan", newsize ) ; |
---|
| 1879 | |
---|
| 1880 | // update bandwidth |
---|
| 1881 | // assumed all spectra in the scantable have same bandwidth |
---|
| 1882 | table_.rwKeywordSet().define( "Bandwidth", increment * newsize ) ; |
---|
| 1883 | |
---|
| 1884 | return ; |
---|
| 1885 | } |
---|
| 1886 | |
---|
| 1887 | void asap::Scantable::reshapeSpectrum( int nmin, int nmax, int irow ) |
---|
| 1888 | { |
---|
| 1889 | // reshape specCol_ and flagCol_ |
---|
| 1890 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
| 1891 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
[2475] | 1892 | Vector<Float> oldtsys = tsysCol_( irow ) ; |
---|
[1819] | 1893 | uInt newsize = nmax - nmin + 1 ; |
---|
[2475] | 1894 | Slice slice( nmin, newsize, 1 ) ; |
---|
| 1895 | specCol_.put( irow, oldspec( slice ) ) ; |
---|
| 1896 | flagsCol_.put( irow, oldflag( slice ) ) ; |
---|
| 1897 | if ( oldspec.size() == oldtsys.size() ) |
---|
| 1898 | tsysCol_.put( irow, oldtsys( slice ) ) ; |
---|
[1819] | 1899 | |
---|
| 1900 | return ; |
---|
| 1901 | } |
---|
| 1902 | |
---|
[2435] | 1903 | void asap::Scantable::regridSpecChannel( double dnu, int nChan ) |
---|
| 1904 | { |
---|
| 1905 | LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ; |
---|
| 1906 | os << "Regrid abcissa with spectral resoultion " << dnu << " " << freqTable_.getUnitString() << " with channel number " << ((nChan>0)? String(nChan) : "covering band width")<< LogIO::POST ; |
---|
| 1907 | int freqnrow = freqTable_.table().nrow() ; |
---|
| 1908 | Vector<bool> firstTime( freqnrow, true ) ; |
---|
| 1909 | double oldincr, factor; |
---|
| 1910 | uInt currId; |
---|
| 1911 | Double refpix ; |
---|
| 1912 | Double refval ; |
---|
| 1913 | Double increment ; |
---|
| 1914 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
| 1915 | currId = mfreqidCol_(irow); |
---|
| 1916 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
| 1917 | if (nChan < 0) { |
---|
| 1918 | int oldsize = abcissa.size() ; |
---|
| 1919 | double bw = (abcissa[oldsize-1]-abcissa[0]) + \ |
---|
| 1920 | 0.5 * (abcissa[1]-abcissa[0] + abcissa[oldsize-1]-abcissa[oldsize-2]) ; |
---|
| 1921 | nChan = int( ceil( abs(bw/dnu) ) ) ; |
---|
| 1922 | } |
---|
| 1923 | // actual regridding |
---|
| 1924 | regridChannel( nChan, dnu, irow ) ; |
---|
[2433] | 1925 | |
---|
[2435] | 1926 | // update FREQUENCIES subtable |
---|
| 1927 | if (firstTime[currId]) { |
---|
| 1928 | oldincr = abcissa[1]-abcissa[0] ; |
---|
| 1929 | factor = dnu/oldincr ; |
---|
| 1930 | firstTime[currId] = false ; |
---|
| 1931 | freqTable_.getEntry( refpix, refval, increment, currId ) ; |
---|
[2463] | 1932 | |
---|
[2437] | 1933 | //refval = refval - ( refpix + 0.5 * (1 - factor) ) * increment ; |
---|
[2463] | 1934 | if (factor > 0 ) { |
---|
[2462] | 1935 | refpix = (refpix + 0.5)/factor - 0.5; |
---|
| 1936 | } else { |
---|
[2463] | 1937 | refpix = (abcissa.size() - 0.5 - refpix)/abs(factor) - 0.5; |
---|
[2462] | 1938 | } |
---|
[2435] | 1939 | freqTable_.setEntry( refpix, refval, increment*factor, currId ) ; |
---|
[2463] | 1940 | //os << "ID" << currId << ": channel width (Orig) = " << oldincr << " [" << freqTable_.getUnitString() << "], scale factor = " << factor << LogIO::POST ; |
---|
| 1941 | //os << " frequency increment (Orig) = " << increment << "-> (New) " << increment*factor << LogIO::POST ; |
---|
[2435] | 1942 | } |
---|
| 1943 | } |
---|
| 1944 | } |
---|
| 1945 | |
---|
[1819] | 1946 | void asap::Scantable::regridChannel( int nChan, double dnu ) |
---|
| 1947 | { |
---|
| 1948 | LogIO os( LogOrigin( "Scantable", "regridChannel()", WHERE ) ) ; |
---|
| 1949 | os << "Regrid abcissa with channel number " << nChan << " and spectral resoultion " << dnu << "Hz." << LogIO::POST ; |
---|
| 1950 | // assumed that all rows have same nChan |
---|
| 1951 | Vector<Float> arr = specCol_( 0 ) ; |
---|
| 1952 | int oldsize = arr.nelements() ; |
---|
| 1953 | |
---|
| 1954 | // if oldsize == nChan, nothing to do |
---|
| 1955 | if ( oldsize == nChan ) { |
---|
| 1956 | os << "Specified channel number is same as current one. Nothing to do." << LogIO::POST ; |
---|
| 1957 | return ; |
---|
| 1958 | } |
---|
| 1959 | |
---|
| 1960 | // if oldChan < nChan, unphysical operation |
---|
| 1961 | if ( oldsize < nChan ) { |
---|
| 1962 | os << "Unphysical operation. Nothing to do." << LogIO::POST ; |
---|
| 1963 | return ; |
---|
| 1964 | } |
---|
| 1965 | |
---|
[2433] | 1966 | // change channel number for specCol_, flagCol_, and tsysCol_ (if necessary) |
---|
[1819] | 1967 | vector<string> coordinfo = getCoordInfo() ; |
---|
| 1968 | string oldinfo = coordinfo[0] ; |
---|
| 1969 | coordinfo[0] = "Hz" ; |
---|
| 1970 | setCoordInfo( coordinfo ) ; |
---|
| 1971 | for ( int irow = 0 ; irow < nrow() ; irow++ ) { |
---|
| 1972 | regridChannel( nChan, dnu, irow ) ; |
---|
| 1973 | } |
---|
| 1974 | coordinfo[0] = oldinfo ; |
---|
| 1975 | setCoordInfo( coordinfo ) ; |
---|
| 1976 | |
---|
| 1977 | |
---|
| 1978 | // NOTE: this method does not update metadata such as |
---|
| 1979 | // FREQUENCIES subtable, nChan, Bandwidth, etc. |
---|
| 1980 | |
---|
| 1981 | return ; |
---|
| 1982 | } |
---|
| 1983 | |
---|
| 1984 | void asap::Scantable::regridChannel( int nChan, double dnu, int irow ) |
---|
| 1985 | { |
---|
| 1986 | // logging |
---|
| 1987 | //ofstream ofs( "average.log", std::ios::out | std::ios::app ) ; |
---|
| 1988 | //ofs << "IFNO = " << getIF( irow ) << " irow = " << irow << endl ; |
---|
| 1989 | |
---|
| 1990 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
| 1991 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
[2431] | 1992 | Vector<Float> oldtsys = tsysCol_( irow ) ; |
---|
[1819] | 1993 | Vector<Float> newspec( nChan, 0 ) ; |
---|
[2431] | 1994 | Vector<uChar> newflag( nChan, true ) ; |
---|
| 1995 | Vector<Float> newtsys ; |
---|
| 1996 | bool regridTsys = false ; |
---|
| 1997 | if (oldtsys.size() == oldspec.size()) { |
---|
| 1998 | regridTsys = true ; |
---|
| 1999 | newtsys.resize(nChan,false) ; |
---|
| 2000 | newtsys = 0 ; |
---|
| 2001 | } |
---|
[1819] | 2002 | |
---|
| 2003 | // regrid |
---|
| 2004 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
| 2005 | int oldsize = abcissa.size() ; |
---|
| 2006 | double olddnu = abcissa[1] - abcissa[0] ; |
---|
[2462] | 2007 | //int ichan = 0 ; |
---|
[1819] | 2008 | double wsum = 0.0 ; |
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[2433] | 2009 | Vector<double> zi( nChan+1 ) ; |
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| 2010 | Vector<double> yi( oldsize + 1 ) ; |
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[1819] | 2011 | yi[0] = abcissa[0] - 0.5 * olddnu ; |
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[2431] | 2012 | for ( int ii = 1 ; ii < oldsize ; ii++ ) |
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[2433] | 2013 | yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ; |
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| 2014 | yi[oldsize] = abcissa[oldsize-1] \ |
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| 2015 | + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ; |
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[2462] | 2016 | //zi[0] = abcissa[0] - 0.5 * olddnu ; |
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| 2017 | zi[0] = ((olddnu*dnu > 0) ? yi[0] : yi[oldsize]) ; |
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| 2018 | for ( int ii = 1 ; ii < nChan ; ii++ ) |
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| 2019 | zi[ii] = zi[0] + dnu * ii ; |
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| 2020 | zi[nChan] = zi[nChan-1] + dnu ; |
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| 2021 | // Access zi and yi in ascending order |
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| 2022 | int izs = ((dnu > 0) ? 0 : nChan ) ; |
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| 2023 | int ize = ((dnu > 0) ? nChan : 0 ) ; |
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| 2024 | int izincr = ((dnu > 0) ? 1 : -1 ) ; |
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| 2025 | int ichan = ((olddnu > 0) ? 0 : oldsize ) ; |
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| 2026 | int iye = ((olddnu > 0) ? oldsize : 0 ) ; |
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| 2027 | int iyincr = ((olddnu > 0) ? 1 : -1 ) ; |
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| 2028 | //for ( int ii = izs ; ii != ize ; ii+=izincr ){ |
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| 2029 | int ii = izs ; |
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| 2030 | while (ii != ize) { |
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| 2031 | // always zl < zr |
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| 2032 | double zl = zi[ii] ; |
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| 2033 | double zr = zi[ii+izincr] ; |
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| 2034 | // Need to access smaller index for the new spec, flag, and tsys. |
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| 2035 | // Values between zi[k] and zi[k+1] should be stored in newspec[k], etc. |
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| 2036 | int i = min(ii, ii+izincr) ; |
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| 2037 | //for ( int jj = ichan ; jj != iye ; jj+=iyincr ) { |
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| 2038 | int jj = ichan ; |
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| 2039 | while (jj != iye) { |
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| 2040 | // always yl < yr |
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| 2041 | double yl = yi[jj] ; |
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| 2042 | double yr = yi[jj+iyincr] ; |
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| 2043 | // Need to access smaller index for the original spec, flag, and tsys. |
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| 2044 | // Values between yi[k] and yi[k+1] are stored in oldspec[k], etc. |
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| 2045 | int j = min(jj, jj+iyincr) ; |
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| 2046 | if ( yr <= zl ) { |
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| 2047 | jj += iyincr ; |
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| 2048 | continue ; |
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[1819] | 2049 | } |
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[2462] | 2050 | else if ( yl <= zl ) { |
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| 2051 | if ( yr < zr ) { |
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| 2052 | if (!oldflag[j]) { |
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| 2053 | newspec[i] += oldspec[j] * ( yr - zl ) ; |
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| 2054 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - zl ) ; |
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| 2055 | wsum += ( yr - zl ) ; |
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| 2056 | } |
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| 2057 | newflag[i] = newflag[i] && oldflag[j] ; |
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| 2058 | } |
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| 2059 | else { |
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| 2060 | if (!oldflag[j]) { |
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| 2061 | newspec[i] += oldspec[j] * abs(dnu) ; |
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| 2062 | if (regridTsys) newtsys[i] += oldtsys[j] * abs(dnu) ; |
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| 2063 | wsum += abs(dnu) ; |
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| 2064 | } |
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| 2065 | newflag[i] = newflag[i] && oldflag[j] ; |
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| 2066 | ichan = jj ; |
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| 2067 | break ; |
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| 2068 | } |
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[2431] | 2069 | } |
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[2462] | 2070 | else if ( yl < zr ) { |
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| 2071 | if ( yr <= zr ) { |
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| 2072 | if (!oldflag[j]) { |
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| 2073 | newspec[i] += oldspec[j] * ( yr - yl ) ; |
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| 2074 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - yl ) ; |
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| 2075 | wsum += ( yr - yl ) ; |
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| 2076 | } |
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| 2077 | newflag[i] = newflag[i] && oldflag[j] ; |
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| 2078 | } |
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| 2079 | else { |
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| 2080 | if (!oldflag[j]) { |
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| 2081 | newspec[i] += oldspec[j] * ( zr - yl ) ; |
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| 2082 | if (regridTsys) newtsys[i] += oldtsys[j] * ( zr - yl ) ; |
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| 2083 | wsum += ( zr - yl ) ; |
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| 2084 | } |
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| 2085 | newflag[i] = newflag[i] && oldflag[j] ; |
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| 2086 | ichan = jj ; |
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| 2087 | break ; |
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| 2088 | } |
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[1819] | 2089 | } |
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[2462] | 2090 | else { |
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| 2091 | ichan = jj - iyincr ; |
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| 2092 | break ; |
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[2431] | 2093 | } |
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[2462] | 2094 | jj += iyincr ; |
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[1819] | 2095 | } |
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[2462] | 2096 | if ( wsum != 0.0 ) { |
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| 2097 | newspec[i] /= wsum ; |
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| 2098 | if (regridTsys) newtsys[i] /= wsum ; |
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| 2099 | } |
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| 2100 | wsum = 0.0 ; |
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| 2101 | ii += izincr ; |
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[1819] | 2102 | } |
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[2462] | 2103 | // if ( dnu > 0.0 ) { |
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| 2104 | // for ( int ii = 0 ; ii < nChan ; ii++ ) { |
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| 2105 | // double zl = zi[ii] ; |
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| 2106 | // double zr = zi[ii+1] ; |
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| 2107 | // for ( int j = ichan ; j < oldsize ; j++ ) { |
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| 2108 | // double yl = yi[j] ; |
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| 2109 | // double yr = yi[j+1] ; |
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| 2110 | // if ( yl <= zl ) { |
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| 2111 | // if ( yr <= zl ) { |
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| 2112 | // continue ; |
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| 2113 | // } |
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| 2114 | // else if ( yr <= zr ) { |
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| 2115 | // if (!oldflag[j]) { |
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| 2116 | // newspec[ii] += oldspec[j] * ( yr - zl ) ; |
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| 2117 | // if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - zl ) ; |
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| 2118 | // wsum += ( yr - zl ) ; |
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| 2119 | // } |
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| 2120 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
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| 2121 | // } |
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| 2122 | // else { |
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| 2123 | // if (!oldflag[j]) { |
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| 2124 | // newspec[ii] += oldspec[j] * dnu ; |
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| 2125 | // if (regridTsys) newtsys[ii] += oldtsys[j] * dnu ; |
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| 2126 | // wsum += dnu ; |
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| 2127 | // } |
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| 2128 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
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| 2129 | // ichan = j ; |
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| 2130 | // break ; |
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| 2131 | // } |
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| 2132 | // } |
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| 2133 | // else if ( yl < zr ) { |
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| 2134 | // if ( yr <= zr ) { |
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| 2135 | // if (!oldflag[j]) { |
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| 2136 | // newspec[ii] += oldspec[j] * ( yr - yl ) ; |
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| 2137 | // if (regridTsys) newtsys[ii] += oldtsys[j] * ( yr - yl ) ; |
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| 2138 | // wsum += ( yr - yl ) ; |
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| 2139 | // } |
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| 2140 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
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| 2141 | // } |
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| 2142 | // else { |
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| 2143 | // if (!oldflag[j]) { |
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| 2144 | // newspec[ii] += oldspec[j] * ( zr - yl ) ; |
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| 2145 | // if (regridTsys) newtsys[ii] += oldtsys[j] * ( zr - yl ) ; |
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| 2146 | // wsum += ( zr - yl ) ; |
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| 2147 | // } |
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| 2148 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
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| 2149 | // ichan = j ; |
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| 2150 | // break ; |
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| 2151 | // } |
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| 2152 | // } |
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| 2153 | // else { |
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| 2154 | // ichan = j - 1 ; |
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| 2155 | // break ; |
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| 2156 | // } |
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| 2157 | // } |
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| 2158 | // if ( wsum != 0.0 ) { |
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| 2159 | // newspec[ii] /= wsum ; |
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| 2160 | // if (regridTsys) newtsys[ii] /= wsum ; |
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| 2161 | // } |
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| 2162 | // wsum = 0.0 ; |
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| 2163 | // } |
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[1819] | 2164 | // } |
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[2462] | 2165 | // else if ( dnu < 0.0 ) { |
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| 2166 | // for ( int ii = 0 ; ii < nChan ; ii++ ) { |
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| 2167 | // double zl = zi[ii] ; |
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| 2168 | // double zr = zi[ii+1] ; |
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| 2169 | // for ( int j = ichan ; j < oldsize ; j++ ) { |
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| 2170 | // double yl = yi[j] ; |
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| 2171 | // double yr = yi[j+1] ; |
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| 2172 | // if ( yl >= zl ) { |
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| 2173 | // if ( yr >= zl ) { |
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| 2174 | // continue ; |
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| 2175 | // } |
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| 2176 | // else if ( yr >= zr ) { |
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| 2177 | // if (!oldflag[j]) { |
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| 2178 | // newspec[ii] += oldspec[j] * abs( yr - zl ) ; |
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| 2179 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - zl ) ; |
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| 2180 | // wsum += abs( yr - zl ) ; |
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| 2181 | // } |
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| 2182 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
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| 2183 | // } |
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| 2184 | // else { |
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| 2185 | // if (!oldflag[j]) { |
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| 2186 | // newspec[ii] += oldspec[j] * abs( dnu ) ; |
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| 2187 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( dnu ) ; |
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| 2188 | // wsum += abs( dnu ) ; |
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| 2189 | // } |
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| 2190 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
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| 2191 | // ichan = j ; |
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| 2192 | // break ; |
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| 2193 | // } |
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| 2194 | // } |
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| 2195 | // else if ( yl > zr ) { |
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| 2196 | // if ( yr >= zr ) { |
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| 2197 | // if (!oldflag[j]) { |
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| 2198 | // newspec[ii] += oldspec[j] * abs( yr - yl ) ; |
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| 2199 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( yr - yl ) ; |
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| 2200 | // wsum += abs( yr - yl ) ; |
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| 2201 | // } |
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| 2202 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
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| 2203 | // } |
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| 2204 | // else { |
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| 2205 | // if (!oldflag[j]) { |
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| 2206 | // newspec[ii] += oldspec[j] * abs( zr - yl ) ; |
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| 2207 | // if (regridTsys) newtsys[ii] += oldtsys[j] * abs( zr - yl ) ; |
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| 2208 | // wsum += abs( zr - yl ) ; |
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| 2209 | // } |
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| 2210 | // newflag[ii] = newflag[ii] && oldflag[j] ; |
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| 2211 | // ichan = j ; |
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| 2212 | // break ; |
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| 2213 | // } |
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| 2214 | // } |
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| 2215 | // else { |
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| 2216 | // ichan = j - 1 ; |
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| 2217 | // break ; |
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| 2218 | // } |
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| 2219 | // } |
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| 2220 | // if ( wsum != 0.0 ) { |
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| 2221 | // newspec[ii] /= wsum ; |
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| 2222 | // if (regridTsys) newtsys[ii] /= wsum ; |
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| 2223 | // } |
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| 2224 | // wsum = 0.0 ; |
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[1819] | 2225 | // } |
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| 2226 | // } |
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[2462] | 2227 | // // //ofs << "olddnu = " << olddnu << ", dnu = " << dnu << endl ; |
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| 2228 | // // pile += dnu ; |
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| 2229 | // // wedge = olddnu * ( refChan + 1 ) ; |
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| 2230 | // // while ( wedge < pile ) { |
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| 2231 | // // newspec[0] += olddnu * oldspec[refChan] ; |
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| 2232 | // // newflag[0] = newflag[0] || oldflag[refChan] ; |
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| 2233 | // // //ofs << "channel " << refChan << " is included in new channel 0" << endl ; |
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| 2234 | // // refChan++ ; |
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| 2235 | // // wedge += olddnu ; |
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| 2236 | // // wsum += olddnu ; |
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| 2237 | // // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
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| 2238 | // // } |
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| 2239 | // // frac = ( wedge - pile ) / olddnu ; |
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| 2240 | // // wsum += ( 1.0 - frac ) * olddnu ; |
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| 2241 | // // newspec[0] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
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| 2242 | // // newflag[0] = newflag[0] || oldflag[refChan] ; |
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| 2243 | // // //ofs << "channel " << refChan << " is partly included in new channel 0" << " with fraction of " << ( 1.0 - frac ) << endl ; |
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| 2244 | // // //ofs << "newspec[0] = " << newspec[0] << " wsum = " << wsum << endl ; |
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| 2245 | // // newspec[0] /= wsum ; |
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| 2246 | // // //ofs << "newspec[0] = " << newspec[0] << endl ; |
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| 2247 | // // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
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[1819] | 2248 | |
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[2462] | 2249 | // // /*** |
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| 2250 | // // * ichan = 1 - nChan-2 |
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| 2251 | // // ***/ |
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| 2252 | // // for ( int ichan = 1 ; ichan < nChan - 1 ; ichan++ ) { |
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| 2253 | // // pile += dnu ; |
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| 2254 | // // newspec[ichan] += frac * olddnu * oldspec[refChan] ; |
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| 2255 | // // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
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| 2256 | // // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << frac << endl ; |
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| 2257 | // // refChan++ ; |
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| 2258 | // // wedge += olddnu ; |
---|
| 2259 | // // wsum = frac * olddnu ; |
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| 2260 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 2261 | // // while ( wedge < pile ) { |
---|
| 2262 | // // newspec[ichan] += olddnu * oldspec[refChan] ; |
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| 2263 | // // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
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| 2264 | // // //ofs << "channel " << refChan << " is included in new channel " << ichan << endl ; |
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| 2265 | // // refChan++ ; |
---|
| 2266 | // // wedge += olddnu ; |
---|
| 2267 | // // wsum += olddnu ; |
---|
| 2268 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 2269 | // // } |
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| 2270 | // // frac = ( wedge - pile ) / olddnu ; |
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| 2271 | // // wsum += ( 1.0 - frac ) * olddnu ; |
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| 2272 | // // newspec[ichan] += ( 1.0 - frac ) * olddnu * oldspec[refChan] ; |
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| 2273 | // // newflag[ichan] = newflag[ichan] || oldflag[refChan] ; |
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| 2274 | // // //ofs << "channel " << refChan << " is partly included in new channel " << ichan << " with fraction of " << ( 1.0 - frac ) << endl ; |
---|
| 2275 | // // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
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| 2276 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << " wsum = " << wsum << endl ; |
---|
| 2277 | // // newspec[ichan] /= wsum ; |
---|
| 2278 | // // //ofs << "newspec[" << ichan << "] = " << newspec[ichan] << endl ; |
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| 2279 | // // } |
---|
[1819] | 2280 | |
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[2462] | 2281 | // // /*** |
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| 2282 | // // * ichan = nChan-1 |
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| 2283 | // // ***/ |
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| 2284 | // // // NOTE: Assumed that all spectra have the same bandwidth |
---|
| 2285 | // // pile += dnu ; |
---|
| 2286 | // // newspec[nChan-1] += frac * olddnu * oldspec[refChan] ; |
---|
| 2287 | // // newflag[nChan-1] = newflag[nChan-1] || oldflag[refChan] ; |
---|
| 2288 | // // //ofs << "channel " << refChan << " is partly included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
| 2289 | // // refChan++ ; |
---|
| 2290 | // // wedge += olddnu ; |
---|
| 2291 | // // wsum = frac * olddnu ; |
---|
| 2292 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 2293 | // // for ( int jchan = refChan ; jchan < oldsize ; jchan++ ) { |
---|
| 2294 | // // newspec[nChan-1] += olddnu * oldspec[jchan] ; |
---|
| 2295 | // // newflag[nChan-1] = newflag[nChan-1] || oldflag[jchan] ; |
---|
| 2296 | // // wsum += olddnu ; |
---|
| 2297 | // // //ofs << "channel " << jchan << " is included in new channel " << nChan-1 << " with fraction of " << frac << endl ; |
---|
| 2298 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 2299 | // // } |
---|
| 2300 | // // //ofs << "wedge = " << wedge << ", pile = " << pile << endl ; |
---|
| 2301 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << " wsum = " << wsum << endl ; |
---|
| 2302 | // // newspec[nChan-1] /= wsum ; |
---|
| 2303 | // // //ofs << "newspec[" << nChan - 1 << "] = " << newspec[nChan-1] << endl ; |
---|
[1819] | 2304 | |
---|
[2462] | 2305 | // // // ofs.close() ; |
---|
| 2306 | |
---|
[2032] | 2307 | specCol_.put( irow, newspec ) ; |
---|
| 2308 | flagsCol_.put( irow, newflag ) ; |
---|
[2431] | 2309 | if (regridTsys) tsysCol_.put( irow, newtsys ); |
---|
[1819] | 2310 | |
---|
| 2311 | return ; |
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| 2312 | } |
---|
| 2313 | |
---|
[2595] | 2314 | void Scantable::regridChannel( int nChan, double dnu, double fmin, int irow ) |
---|
| 2315 | { |
---|
| 2316 | Vector<Float> oldspec = specCol_( irow ) ; |
---|
| 2317 | Vector<uChar> oldflag = flagsCol_( irow ) ; |
---|
| 2318 | Vector<Float> oldtsys = tsysCol_( irow ) ; |
---|
| 2319 | Vector<Float> newspec( nChan, 0 ) ; |
---|
| 2320 | Vector<uChar> newflag( nChan, true ) ; |
---|
| 2321 | Vector<Float> newtsys ; |
---|
| 2322 | bool regridTsys = false ; |
---|
| 2323 | if (oldtsys.size() == oldspec.size()) { |
---|
| 2324 | regridTsys = true ; |
---|
| 2325 | newtsys.resize(nChan,false) ; |
---|
| 2326 | newtsys = 0 ; |
---|
| 2327 | } |
---|
| 2328 | |
---|
| 2329 | // regrid |
---|
| 2330 | vector<double> abcissa = getAbcissa( irow ) ; |
---|
| 2331 | int oldsize = abcissa.size() ; |
---|
| 2332 | double olddnu = abcissa[1] - abcissa[0] ; |
---|
| 2333 | //int ichan = 0 ; |
---|
| 2334 | double wsum = 0.0 ; |
---|
| 2335 | Vector<double> zi( nChan+1 ) ; |
---|
| 2336 | Vector<double> yi( oldsize + 1 ) ; |
---|
| 2337 | Block<uInt> count( nChan, 0 ) ; |
---|
| 2338 | yi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
| 2339 | for ( int ii = 1 ; ii < oldsize ; ii++ ) |
---|
| 2340 | yi[ii] = 0.5* (abcissa[ii-1] + abcissa[ii]) ; |
---|
| 2341 | yi[oldsize] = abcissa[oldsize-1] \ |
---|
| 2342 | + 0.5 * (abcissa[oldsize-1] - abcissa[oldsize-2]) ; |
---|
| 2343 | // cout << "olddnu=" << olddnu << ", dnu=" << dnu << " (diff=" << olddnu-dnu << ")" << endl ; |
---|
| 2344 | // cout << "yi[0]=" << yi[0] << ", fmin=" << fmin << " (diff=" << yi[0]-fmin << ")" << endl ; |
---|
| 2345 | // cout << "oldsize=" << oldsize << ", nChan=" << nChan << endl ; |
---|
| 2346 | |
---|
| 2347 | // do not regrid if input parameters are almost same as current |
---|
| 2348 | // spectral setup |
---|
| 2349 | double dnuDiff = abs( ( dnu - olddnu ) / olddnu ) ; |
---|
| 2350 | double oldfmin = min( yi[0], yi[oldsize] ) ; |
---|
| 2351 | double fminDiff = abs( ( fmin - oldfmin ) / oldfmin ) ; |
---|
| 2352 | double nChanDiff = nChan - oldsize ; |
---|
| 2353 | double eps = 1.0e-8 ; |
---|
| 2354 | if ( nChanDiff == 0 && dnuDiff < eps && fminDiff < eps ) |
---|
| 2355 | return ; |
---|
| 2356 | |
---|
| 2357 | //zi[0] = abcissa[0] - 0.5 * olddnu ; |
---|
| 2358 | //zi[0] = ((olddnu*dnu > 0) ? yi[0] : yi[oldsize]) ; |
---|
| 2359 | if ( dnu > 0 ) |
---|
| 2360 | zi[0] = fmin - 0.5 * dnu ; |
---|
| 2361 | else |
---|
| 2362 | zi[0] = fmin + nChan * abs(dnu) ; |
---|
| 2363 | for ( int ii = 1 ; ii < nChan ; ii++ ) |
---|
| 2364 | zi[ii] = zi[0] + dnu * ii ; |
---|
| 2365 | zi[nChan] = zi[nChan-1] + dnu ; |
---|
| 2366 | // Access zi and yi in ascending order |
---|
| 2367 | int izs = ((dnu > 0) ? 0 : nChan ) ; |
---|
| 2368 | int ize = ((dnu > 0) ? nChan : 0 ) ; |
---|
| 2369 | int izincr = ((dnu > 0) ? 1 : -1 ) ; |
---|
| 2370 | int ichan = ((olddnu > 0) ? 0 : oldsize ) ; |
---|
| 2371 | int iye = ((olddnu > 0) ? oldsize : 0 ) ; |
---|
| 2372 | int iyincr = ((olddnu > 0) ? 1 : -1 ) ; |
---|
| 2373 | //for ( int ii = izs ; ii != ize ; ii+=izincr ){ |
---|
| 2374 | int ii = izs ; |
---|
| 2375 | while (ii != ize) { |
---|
| 2376 | // always zl < zr |
---|
| 2377 | double zl = zi[ii] ; |
---|
| 2378 | double zr = zi[ii+izincr] ; |
---|
| 2379 | // Need to access smaller index for the new spec, flag, and tsys. |
---|
| 2380 | // Values between zi[k] and zi[k+1] should be stored in newspec[k], etc. |
---|
| 2381 | int i = min(ii, ii+izincr) ; |
---|
| 2382 | //for ( int jj = ichan ; jj != iye ; jj+=iyincr ) { |
---|
| 2383 | int jj = ichan ; |
---|
| 2384 | while (jj != iye) { |
---|
| 2385 | // always yl < yr |
---|
| 2386 | double yl = yi[jj] ; |
---|
| 2387 | double yr = yi[jj+iyincr] ; |
---|
| 2388 | // Need to access smaller index for the original spec, flag, and tsys. |
---|
| 2389 | // Values between yi[k] and yi[k+1] are stored in oldspec[k], etc. |
---|
| 2390 | int j = min(jj, jj+iyincr) ; |
---|
| 2391 | if ( yr <= zl ) { |
---|
| 2392 | jj += iyincr ; |
---|
| 2393 | continue ; |
---|
| 2394 | } |
---|
| 2395 | else if ( yl <= zl ) { |
---|
| 2396 | if ( yr < zr ) { |
---|
| 2397 | if (!oldflag[j]) { |
---|
| 2398 | newspec[i] += oldspec[j] * ( yr - zl ) ; |
---|
| 2399 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - zl ) ; |
---|
| 2400 | wsum += ( yr - zl ) ; |
---|
| 2401 | count[i]++ ; |
---|
| 2402 | } |
---|
| 2403 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
| 2404 | } |
---|
| 2405 | else { |
---|
| 2406 | if (!oldflag[j]) { |
---|
| 2407 | newspec[i] += oldspec[j] * abs(dnu) ; |
---|
| 2408 | if (regridTsys) newtsys[i] += oldtsys[j] * abs(dnu) ; |
---|
| 2409 | wsum += abs(dnu) ; |
---|
| 2410 | count[i]++ ; |
---|
| 2411 | } |
---|
| 2412 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
| 2413 | ichan = jj ; |
---|
| 2414 | break ; |
---|
| 2415 | } |
---|
| 2416 | } |
---|
| 2417 | else if ( yl < zr ) { |
---|
| 2418 | if ( yr <= zr ) { |
---|
| 2419 | if (!oldflag[j]) { |
---|
| 2420 | newspec[i] += oldspec[j] * ( yr - yl ) ; |
---|
| 2421 | if (regridTsys) newtsys[i] += oldtsys[j] * ( yr - yl ) ; |
---|
| 2422 | wsum += ( yr - yl ) ; |
---|
| 2423 | count[i]++ ; |
---|
| 2424 | } |
---|
| 2425 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
| 2426 | } |
---|
| 2427 | else { |
---|
| 2428 | if (!oldflag[j]) { |
---|
| 2429 | newspec[i] += oldspec[j] * ( zr - yl ) ; |
---|
| 2430 | if (regridTsys) newtsys[i] += oldtsys[j] * ( zr - yl ) ; |
---|
| 2431 | wsum += ( zr - yl ) ; |
---|
| 2432 | count[i]++ ; |
---|
| 2433 | } |
---|
| 2434 | newflag[i] = newflag[i] && oldflag[j] ; |
---|
| 2435 | ichan = jj ; |
---|
| 2436 | break ; |
---|
| 2437 | } |
---|
| 2438 | } |
---|
| 2439 | else { |
---|
| 2440 | //ichan = jj - iyincr ; |
---|
| 2441 | break ; |
---|
| 2442 | } |
---|
| 2443 | jj += iyincr ; |
---|
| 2444 | } |
---|
| 2445 | if ( wsum != 0.0 ) { |
---|
| 2446 | newspec[i] /= wsum ; |
---|
| 2447 | if (regridTsys) newtsys[i] /= wsum ; |
---|
| 2448 | } |
---|
| 2449 | wsum = 0.0 ; |
---|
| 2450 | ii += izincr ; |
---|
| 2451 | } |
---|
| 2452 | |
---|
| 2453 | // flag out channels without data |
---|
| 2454 | // this is tentative since there is no specific definition |
---|
| 2455 | // on bit flag... |
---|
| 2456 | uChar noData = 1 << 7 ; |
---|
| 2457 | for ( Int i = 0 ; i < nChan ; i++ ) { |
---|
| 2458 | if ( count[i] == 0 ) |
---|
| 2459 | newflag[i] = noData ; |
---|
| 2460 | } |
---|
| 2461 | |
---|
| 2462 | specCol_.put( irow, newspec ) ; |
---|
| 2463 | flagsCol_.put( irow, newflag ) ; |
---|
| 2464 | if (regridTsys) tsysCol_.put( irow, newtsys ); |
---|
| 2465 | |
---|
| 2466 | return ; |
---|
| 2467 | } |
---|
| 2468 | |
---|
[1730] | 2469 | std::vector<float> Scantable::getWeather(int whichrow) const |
---|
| 2470 | { |
---|
| 2471 | std::vector<float> out(5); |
---|
| 2472 | //Float temperature, pressure, humidity, windspeed, windaz; |
---|
| 2473 | weatherTable_.getEntry(out[0], out[1], out[2], out[3], out[4], |
---|
| 2474 | mweatheridCol_(uInt(whichrow))); |
---|
| 2475 | |
---|
| 2476 | |
---|
| 2477 | return out; |
---|
[1391] | 2478 | } |
---|
[1730] | 2479 | |
---|
[2047] | 2480 | bool Scantable::getFlagtraFast(uInt whichrow) |
---|
[1907] | 2481 | { |
---|
| 2482 | uChar flag; |
---|
| 2483 | Vector<uChar> flags; |
---|
[2047] | 2484 | flagsCol_.get(whichrow, flags); |
---|
[2012] | 2485 | flag = flags[0]; |
---|
[2047] | 2486 | for (uInt i = 1; i < flags.size(); ++i) { |
---|
[2012] | 2487 | flag &= flags[i]; |
---|
| 2488 | } |
---|
| 2489 | return ((flag >> 7) == 1); |
---|
| 2490 | } |
---|
| 2491 | |
---|
[2277] | 2492 | void Scantable::polyBaseline(const std::vector<bool>& mask, int order, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2047] | 2493 | { |
---|
[2193] | 2494 | try { |
---|
| 2495 | ofstream ofs; |
---|
| 2496 | String coordInfo = ""; |
---|
| 2497 | bool hasSameNchan = true; |
---|
| 2498 | bool outTextFile = false; |
---|
[2641] | 2499 | bool csvFormat = false; |
---|
[2047] | 2500 | |
---|
[2193] | 2501 | if (blfile != "") { |
---|
[2641] | 2502 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
| 2503 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
[2193] | 2504 | if (ofs) outTextFile = true; |
---|
| 2505 | } |
---|
[2047] | 2506 | |
---|
[2193] | 2507 | if (outLogger || outTextFile) { |
---|
| 2508 | coordInfo = getCoordInfo()[0]; |
---|
| 2509 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2510 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2511 | } |
---|
[2047] | 2512 | |
---|
[2193] | 2513 | Fitter fitter = Fitter(); |
---|
| 2514 | fitter.setExpression("poly", order); |
---|
| 2515 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2047] | 2516 | |
---|
[2193] | 2517 | int nRow = nrow(); |
---|
| 2518 | std::vector<bool> chanMask; |
---|
| 2519 | bool showProgress; |
---|
| 2520 | int minNRow; |
---|
| 2521 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2047] | 2522 | |
---|
[2193] | 2523 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 2524 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
| 2525 | fitBaseline(chanMask, whichrow, fitter); |
---|
| 2526 | setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
[2641] | 2527 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "polyBaseline()", fitter); |
---|
[2193] | 2528 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
| 2529 | } |
---|
| 2530 | |
---|
| 2531 | if (outTextFile) ofs.close(); |
---|
| 2532 | |
---|
| 2533 | } catch (...) { |
---|
| 2534 | throw; |
---|
[2047] | 2535 | } |
---|
| 2536 | } |
---|
| 2537 | |
---|
[2189] | 2538 | void Scantable::autoPolyBaseline(const std::vector<bool>& mask, int order, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2047] | 2539 | { |
---|
[2193] | 2540 | try { |
---|
| 2541 | ofstream ofs; |
---|
| 2542 | String coordInfo = ""; |
---|
| 2543 | bool hasSameNchan = true; |
---|
| 2544 | bool outTextFile = false; |
---|
[2641] | 2545 | bool csvFormat = false; |
---|
[2047] | 2546 | |
---|
[2193] | 2547 | if (blfile != "") { |
---|
[2641] | 2548 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
| 2549 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
[2193] | 2550 | if (ofs) outTextFile = true; |
---|
| 2551 | } |
---|
[2047] | 2552 | |
---|
[2193] | 2553 | if (outLogger || outTextFile) { |
---|
| 2554 | coordInfo = getCoordInfo()[0]; |
---|
| 2555 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2556 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2557 | } |
---|
[2047] | 2558 | |
---|
[2193] | 2559 | Fitter fitter = Fitter(); |
---|
| 2560 | fitter.setExpression("poly", order); |
---|
| 2561 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2047] | 2562 | |
---|
[2193] | 2563 | int nRow = nrow(); |
---|
| 2564 | std::vector<bool> chanMask; |
---|
| 2565 | int minEdgeSize = getIFNos().size()*2; |
---|
| 2566 | STLineFinder lineFinder = STLineFinder(); |
---|
| 2567 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
[2047] | 2568 | |
---|
[2193] | 2569 | bool showProgress; |
---|
| 2570 | int minNRow; |
---|
| 2571 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2189] | 2572 | |
---|
[2193] | 2573 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2047] | 2574 | |
---|
[2193] | 2575 | //------------------------------------------------------- |
---|
| 2576 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
| 2577 | //------------------------------------------------------- |
---|
| 2578 | int edgeSize = edge.size(); |
---|
| 2579 | std::vector<int> currentEdge; |
---|
| 2580 | if (edgeSize >= 2) { |
---|
| 2581 | int idx = 0; |
---|
| 2582 | if (edgeSize > 2) { |
---|
| 2583 | if (edgeSize < minEdgeSize) { |
---|
| 2584 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 2585 | } |
---|
| 2586 | idx = 2 * getIF(whichrow); |
---|
[2047] | 2587 | } |
---|
[2193] | 2588 | currentEdge.push_back(edge[idx]); |
---|
| 2589 | currentEdge.push_back(edge[idx+1]); |
---|
| 2590 | } else { |
---|
| 2591 | throw(AipsError("Wrong length of edge element")); |
---|
[2047] | 2592 | } |
---|
[2193] | 2593 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 2594 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
| 2595 | chanMask = lineFinder.getMask(); |
---|
| 2596 | //------------------------------------------------------- |
---|
| 2597 | |
---|
| 2598 | fitBaseline(chanMask, whichrow, fitter); |
---|
| 2599 | setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
| 2600 | |
---|
[2641] | 2601 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoPolyBaseline()", fitter); |
---|
[2193] | 2602 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[2047] | 2603 | } |
---|
| 2604 | |
---|
[2193] | 2605 | if (outTextFile) ofs.close(); |
---|
[2047] | 2606 | |
---|
[2193] | 2607 | } catch (...) { |
---|
| 2608 | throw; |
---|
[2047] | 2609 | } |
---|
| 2610 | } |
---|
| 2611 | |
---|
[2645] | 2612 | void Scantable::chebyshevBaseline(const std::vector<bool>& mask, int order, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
| 2613 | { |
---|
| 2614 | try { |
---|
| 2615 | ofstream ofs; |
---|
| 2616 | String coordInfo = ""; |
---|
| 2617 | bool hasSameNchan = true; |
---|
| 2618 | bool outTextFile = false; |
---|
| 2619 | bool csvFormat = false; |
---|
| 2620 | |
---|
| 2621 | if (blfile != "") { |
---|
| 2622 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
| 2623 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
| 2624 | if (ofs) outTextFile = true; |
---|
| 2625 | } |
---|
| 2626 | |
---|
| 2627 | if (outLogger || outTextFile) { |
---|
| 2628 | coordInfo = getCoordInfo()[0]; |
---|
| 2629 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2630 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2631 | } |
---|
| 2632 | |
---|
| 2633 | bool showProgress; |
---|
| 2634 | int minNRow; |
---|
| 2635 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
| 2636 | |
---|
| 2637 | int nRow = nrow(); |
---|
| 2638 | std::vector<bool> chanMask; |
---|
[2737] | 2639 | std::vector<bool> finalChanMask; |
---|
| 2640 | float rms; |
---|
| 2641 | |
---|
| 2642 | //--- |
---|
[2740] | 2643 | bool outBaselineParamTable = false; |
---|
[2737] | 2644 | STBaselineTable* bt = new STBaselineTable(*this); |
---|
| 2645 | //--- |
---|
| 2646 | |
---|
[2645] | 2647 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 2648 | std::vector<float> sp = getSpectrum(whichrow); |
---|
| 2649 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
| 2650 | std::vector<float> params(order+1); |
---|
| 2651 | int nClipped = 0; |
---|
[2737] | 2652 | std::vector<float> res = doChebyshevFitting(sp, chanMask, order, params, finalChanMask, rms, nClipped, thresClip, nIterClip, getResidual); |
---|
[2645] | 2653 | |
---|
[2737] | 2654 | //--- |
---|
| 2655 | if (outBaselineParamTable) { |
---|
| 2656 | bt->appenddata(uInt(getScan(whichrow)), uInt(getCycle(whichrow)), uInt(getBeam(whichrow)), uInt(getIF(whichrow)), uInt(getPol(whichrow)), |
---|
| 2657 | uInt(0), |
---|
| 2658 | Double(0.0), // <-- Double(getTime(whichrow, false)), |
---|
[2740] | 2659 | uInt(nchan(whichrow)), |
---|
| 2660 | STBaselineFunc::Chebyshev, |
---|
| 2661 | Vector<uInt>(1), // ==> MUST BE Vector<uInt> containing 'order'. |
---|
| 2662 | Vector<Float>(), // ==> for ffpar. ** dummy ** |
---|
| 2663 | uInt(nIterClip), |
---|
| 2664 | Float(thresClip), |
---|
| 2665 | Vector<uInt>(5), // <-- Vector<uInt>(finalChanMask), |
---|
| 2666 | Vector<Float>(params), |
---|
[2737] | 2667 | Float(rms)); |
---|
| 2668 | } else { |
---|
| 2669 | setSpectrum(res, whichrow); |
---|
| 2670 | } |
---|
| 2671 | //--- |
---|
| 2672 | |
---|
[2645] | 2673 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "chebyshevBaseline()", params, nClipped); |
---|
| 2674 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
| 2675 | } |
---|
| 2676 | |
---|
[2737] | 2677 | //--- |
---|
| 2678 | if (outBaselineParamTable) { |
---|
| 2679 | bt->save("chebyparamtable"); |
---|
| 2680 | } |
---|
| 2681 | //--- |
---|
| 2682 | delete bt; |
---|
| 2683 | |
---|
[2645] | 2684 | if (outTextFile) ofs.close(); |
---|
| 2685 | |
---|
| 2686 | } catch (...) { |
---|
| 2687 | throw; |
---|
| 2688 | } |
---|
| 2689 | } |
---|
| 2690 | |
---|
[2713] | 2691 | double Scantable::calculateModelSelectionCriteria(const std::string& valname, const std::string& blfunc, int order, const std::vector<bool>& inMask, int whichrow, bool useLineFinder, const std::vector<int>& edge, float threshold, int chanAvgLimit) |
---|
| 2692 | { |
---|
| 2693 | if (useLineFinder) { |
---|
| 2694 | int minEdgeSize = getIFNos().size()*2; |
---|
| 2695 | |
---|
| 2696 | |
---|
| 2697 | int edgeSize = edge.size(); |
---|
| 2698 | std::vector<int> currentEdge; |
---|
| 2699 | if (edgeSize >= 2) { |
---|
| 2700 | int idx = 0; |
---|
| 2701 | if (edgeSize > 2) { |
---|
| 2702 | if (edgeSize < minEdgeSize) { |
---|
| 2703 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 2704 | } |
---|
| 2705 | idx = 2 * getIF(whichrow); |
---|
| 2706 | } |
---|
| 2707 | currentEdge.push_back(edge[idx]); |
---|
| 2708 | currentEdge.push_back(edge[idx+1]); |
---|
| 2709 | } else { |
---|
| 2710 | throw(AipsError("Wrong length of edge element")); |
---|
| 2711 | } |
---|
| 2712 | |
---|
| 2713 | STLineFinder lineFinder = STLineFinder(); |
---|
| 2714 | std::vector<float> sp = getSpectrum(whichrow); |
---|
| 2715 | lineFinder.setData(sp); |
---|
| 2716 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
| 2717 | lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow); |
---|
| 2718 | std::vector<bool> chanMask = lineFinder.getMask(); |
---|
| 2719 | |
---|
| 2720 | return doCalculateModelSelectionCriteria(valname, sp, chanMask, blfunc, order); |
---|
| 2721 | |
---|
| 2722 | } else { |
---|
| 2723 | return doCalculateModelSelectionCriteria(valname, getSpectrum(whichrow), getCompositeChanMask(whichrow, inMask), blfunc, order); |
---|
| 2724 | } |
---|
| 2725 | |
---|
| 2726 | } |
---|
| 2727 | |
---|
| 2728 | double Scantable::doCalculateModelSelectionCriteria(const std::string& valname, const std::vector<float>& spec, const std::vector<bool>& mask, const std::string& blfunc, int order) |
---|
| 2729 | { |
---|
| 2730 | int nparam; |
---|
| 2731 | std::vector<float> params; |
---|
[2737] | 2732 | std::vector<bool> finalChanMask; |
---|
| 2733 | float rms; |
---|
[2713] | 2734 | int nClipped = 0; |
---|
| 2735 | float thresClip = 0.0; |
---|
| 2736 | int nIterClip = 0; |
---|
| 2737 | std::vector<float> res; |
---|
| 2738 | if (blfunc == "chebyshev") { |
---|
| 2739 | nparam = order + 1; |
---|
[2737] | 2740 | res = doChebyshevFitting(spec, mask, order, params, finalChanMask, rms, nClipped, thresClip, nIterClip, true); |
---|
[2713] | 2741 | } else if (blfunc == "sinusoid") { |
---|
| 2742 | std::vector<int> nWaves; |
---|
| 2743 | nWaves.clear(); |
---|
| 2744 | for (int i = 0; i <= order; ++i) { |
---|
| 2745 | nWaves.push_back(i); |
---|
| 2746 | } |
---|
| 2747 | nparam = 2*order + 1; // order = nwave |
---|
| 2748 | res = doSinusoidFitting(spec, mask, nWaves, params, nClipped, thresClip, nIterClip, true); |
---|
| 2749 | } else if (blfunc == "cspline") { |
---|
| 2750 | std::vector<int> pieceEdges(order+1); //order = npiece |
---|
| 2751 | nparam = order + 3; |
---|
| 2752 | params.resize(4*order); |
---|
| 2753 | res = doCubicSplineFitting(spec, mask, order, pieceEdges, params, nClipped, thresClip, nIterClip, true); |
---|
| 2754 | } else { |
---|
| 2755 | throw(AipsError("blfunc must be chebyshev, cspline or sinusoid.")); |
---|
| 2756 | } |
---|
| 2757 | |
---|
| 2758 | double msq = 0.0; |
---|
| 2759 | int nusedchan = 0; |
---|
| 2760 | int nChan = res.size(); |
---|
| 2761 | for (int i = 0; i < nChan; ++i) { |
---|
| 2762 | if (mask[i]) { |
---|
| 2763 | msq += (double)res[i]*(double)res[i]; |
---|
| 2764 | nusedchan++; |
---|
| 2765 | } |
---|
| 2766 | } |
---|
| 2767 | if (nusedchan == 0) { |
---|
| 2768 | throw(AipsError("all channels masked.")); |
---|
| 2769 | } |
---|
| 2770 | msq /= (double)nusedchan; |
---|
| 2771 | |
---|
| 2772 | nparam++; //add 1 for sigma of Gaussian distribution |
---|
| 2773 | const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...) |
---|
| 2774 | |
---|
| 2775 | if (valname.find("aic") == 0) { |
---|
| 2776 | // Original Akaike Information Criterion (AIC) |
---|
| 2777 | double aic = nusedchan * (log(2.0 * PI * msq) + 1.0) + 2.0 * nparam; |
---|
| 2778 | |
---|
| 2779 | // Corrected AIC by Sugiura(1978) |
---|
| 2780 | if (valname == "aicc") { |
---|
| 2781 | if (nusedchan - nparam - 1 <= 0) { |
---|
| 2782 | throw(AipsError("channel size is too small to calculate AICc.")); |
---|
| 2783 | } |
---|
| 2784 | aic += 2.0*nparam*(nparam + 1)/(double)(nusedchan - nparam - 1); |
---|
| 2785 | } |
---|
| 2786 | |
---|
| 2787 | return aic; |
---|
| 2788 | |
---|
| 2789 | } else if (valname == "bic") { |
---|
| 2790 | // Bayesian Information Criterion (BIC) |
---|
| 2791 | double bic = nusedchan * log(msq) + nparam * log((double)nusedchan); |
---|
| 2792 | return bic; |
---|
| 2793 | |
---|
| 2794 | } else if (valname == "gcv") { |
---|
| 2795 | // Generalised Cross Validation |
---|
| 2796 | double x = 1.0 - (double)nparam / (double)nusedchan; |
---|
| 2797 | double gcv = msq / (x * x); |
---|
| 2798 | return gcv; |
---|
| 2799 | |
---|
| 2800 | } else { |
---|
| 2801 | throw(AipsError("valname must be aic, aicc, bic or gcv.")); |
---|
| 2802 | } |
---|
| 2803 | } |
---|
| 2804 | |
---|
[2645] | 2805 | void Scantable::autoChebyshevBaseline(const std::vector<bool>& mask, int order, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
| 2806 | { |
---|
| 2807 | try { |
---|
| 2808 | ofstream ofs; |
---|
| 2809 | String coordInfo = ""; |
---|
| 2810 | bool hasSameNchan = true; |
---|
| 2811 | bool outTextFile = false; |
---|
| 2812 | bool csvFormat = false; |
---|
| 2813 | |
---|
| 2814 | if (blfile != "") { |
---|
| 2815 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
| 2816 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
| 2817 | if (ofs) outTextFile = true; |
---|
| 2818 | } |
---|
| 2819 | |
---|
| 2820 | if (outLogger || outTextFile) { |
---|
| 2821 | coordInfo = getCoordInfo()[0]; |
---|
| 2822 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 2823 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 2824 | } |
---|
| 2825 | |
---|
| 2826 | int nRow = nrow(); |
---|
| 2827 | std::vector<bool> chanMask; |
---|
| 2828 | int minEdgeSize = getIFNos().size()*2; |
---|
| 2829 | STLineFinder lineFinder = STLineFinder(); |
---|
| 2830 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
| 2831 | |
---|
| 2832 | bool showProgress; |
---|
| 2833 | int minNRow; |
---|
| 2834 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
| 2835 | |
---|
[2737] | 2836 | std::vector<bool> finalChanMask; |
---|
| 2837 | float rms; |
---|
| 2838 | |
---|
[2645] | 2839 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 2840 | std::vector<float> sp = getSpectrum(whichrow); |
---|
| 2841 | |
---|
| 2842 | //------------------------------------------------------- |
---|
| 2843 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
| 2844 | //------------------------------------------------------- |
---|
| 2845 | int edgeSize = edge.size(); |
---|
| 2846 | std::vector<int> currentEdge; |
---|
| 2847 | if (edgeSize >= 2) { |
---|
| 2848 | int idx = 0; |
---|
| 2849 | if (edgeSize > 2) { |
---|
| 2850 | if (edgeSize < minEdgeSize) { |
---|
| 2851 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 2852 | } |
---|
| 2853 | idx = 2 * getIF(whichrow); |
---|
| 2854 | } |
---|
| 2855 | currentEdge.push_back(edge[idx]); |
---|
| 2856 | currentEdge.push_back(edge[idx+1]); |
---|
| 2857 | } else { |
---|
| 2858 | throw(AipsError("Wrong length of edge element")); |
---|
| 2859 | } |
---|
| 2860 | //lineFinder.setData(getSpectrum(whichrow)); |
---|
| 2861 | lineFinder.setData(sp); |
---|
| 2862 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
| 2863 | chanMask = lineFinder.getMask(); |
---|
| 2864 | //------------------------------------------------------- |
---|
| 2865 | |
---|
| 2866 | |
---|
| 2867 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 2868 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
| 2869 | std::vector<float> params(order+1); |
---|
| 2870 | int nClipped = 0; |
---|
[2737] | 2871 | std::vector<float> res = doChebyshevFitting(sp, chanMask, order, params, finalChanMask, rms, nClipped, thresClip, nIterClip, getResidual); |
---|
[2645] | 2872 | setSpectrum(res, whichrow); |
---|
| 2873 | |
---|
| 2874 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoChebyshevBaseline()", params, nClipped); |
---|
| 2875 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
| 2876 | } |
---|
| 2877 | |
---|
| 2878 | if (outTextFile) ofs.close(); |
---|
| 2879 | |
---|
| 2880 | } catch (...) { |
---|
| 2881 | throw; |
---|
| 2882 | } |
---|
| 2883 | } |
---|
| 2884 | |
---|
| 2885 | /* |
---|
| 2886 | double Scantable::getChebyshevPolynomial(int n, double x) { |
---|
| 2887 | if ((x < -1.0)||(x > 1.0)) { |
---|
| 2888 | throw(AipsError("out of definition range (-1 <= x <= 1).")); |
---|
| 2889 | } else if (n < 0) { |
---|
| 2890 | throw(AipsError("the order must be zero or positive.")); |
---|
| 2891 | } else if (n == 0) { |
---|
| 2892 | return 1.0; |
---|
| 2893 | } else if (n == 1) { |
---|
| 2894 | return x; |
---|
| 2895 | } else { |
---|
| 2896 | return 2.0*x*getChebyshevPolynomial(n-1, x) - getChebyshevPolynomial(n-2, x); |
---|
| 2897 | } |
---|
| 2898 | } |
---|
| 2899 | */ |
---|
| 2900 | double Scantable::getChebyshevPolynomial(int n, double x) { |
---|
| 2901 | if ((x < -1.0)||(x > 1.0)) { |
---|
| 2902 | throw(AipsError("out of definition range (-1 <= x <= 1).")); |
---|
[2713] | 2903 | } else if (x == 1.0) { |
---|
| 2904 | return 1.0; |
---|
| 2905 | } else if (x == 0.0) { |
---|
| 2906 | double res; |
---|
| 2907 | if (n%2 == 0) { |
---|
| 2908 | if (n%4 == 0) { |
---|
| 2909 | res = 1.0; |
---|
| 2910 | } else { |
---|
| 2911 | res = -1.0; |
---|
| 2912 | } |
---|
| 2913 | } else { |
---|
| 2914 | res = 0.0; |
---|
| 2915 | } |
---|
| 2916 | return res; |
---|
| 2917 | } else if (x == -1.0) { |
---|
| 2918 | double res = (n%2 == 0 ? 1.0 : -1.0); |
---|
| 2919 | return res; |
---|
[2645] | 2920 | } else if (n < 0) { |
---|
| 2921 | throw(AipsError("the order must be zero or positive.")); |
---|
| 2922 | } else if (n == 0) { |
---|
| 2923 | return 1.0; |
---|
| 2924 | } else if (n == 1) { |
---|
| 2925 | return x; |
---|
| 2926 | } else { |
---|
| 2927 | double res = 0.0; |
---|
| 2928 | for (int m = 0; m <= n/2; ++m) { |
---|
| 2929 | double c = 1.0; |
---|
| 2930 | if (m > 0) { |
---|
| 2931 | for (int i = 1; i <= m; ++i) { |
---|
| 2932 | c *= (double)(n-2*m+i)/(double)i; |
---|
| 2933 | } |
---|
| 2934 | } |
---|
[2713] | 2935 | res += (m%2 == 0 ? 1.0 : -1.0)*(double)n/(double)(n-m)*pow(2.0*x, (double)(n-2*m))/2.0*c; |
---|
[2645] | 2936 | } |
---|
| 2937 | return res; |
---|
| 2938 | } |
---|
| 2939 | } |
---|
| 2940 | |
---|
[2737] | 2941 | std::vector<float> Scantable::doChebyshevFitting(const std::vector<float>& data, const std::vector<bool>& mask, int order, std::vector<float>& params, std::vector<bool>& finalMask, float& rms, int& nClipped, float thresClip, int nIterClip, bool getResidual) |
---|
[2645] | 2942 | { |
---|
| 2943 | if (data.size() != mask.size()) { |
---|
| 2944 | throw(AipsError("data and mask sizes are not identical")); |
---|
| 2945 | } |
---|
| 2946 | if (order < 0) { |
---|
| 2947 | throw(AipsError("maximum order of Chebyshev polynomial must not be negative.")); |
---|
| 2948 | } |
---|
| 2949 | |
---|
| 2950 | int nChan = data.size(); |
---|
[2737] | 2951 | |
---|
| 2952 | finalMask.clear(); |
---|
| 2953 | finalMask.resize(nChan); |
---|
| 2954 | |
---|
[2645] | 2955 | std::vector<int> maskArray; |
---|
| 2956 | std::vector<int> x; |
---|
| 2957 | for (int i = 0; i < nChan; ++i) { |
---|
| 2958 | maskArray.push_back(mask[i] ? 1 : 0); |
---|
| 2959 | if (mask[i]) { |
---|
| 2960 | x.push_back(i); |
---|
| 2961 | } |
---|
[2737] | 2962 | finalMask[i] = mask[i]; |
---|
[2645] | 2963 | } |
---|
| 2964 | |
---|
| 2965 | int initNData = x.size(); |
---|
| 2966 | |
---|
| 2967 | int nData = initNData; |
---|
| 2968 | int nDOF = order + 1; //number of parameters to solve. |
---|
| 2969 | |
---|
| 2970 | // xArray : contains elemental values for computing the least-square matrix. |
---|
| 2971 | // xArray.size() is nDOF and xArray[*].size() is nChan. |
---|
| 2972 | // Each xArray element are as follows: |
---|
| 2973 | // xArray[0] = {T0(-1), T0(2/(nChan-1)-1), T0(4/(nChan-1)-1), ..., T0(1)}, |
---|
| 2974 | // xArray[n-1] = ..., |
---|
| 2975 | // xArray[n] = {Tn(-1), Tn(2/(nChan-1)-1), Tn(4/(nChan-1)-1), ..., Tn(1)} |
---|
| 2976 | // where (0 <= n <= order), |
---|
| 2977 | std::vector<std::vector<double> > xArray; |
---|
| 2978 | for (int i = 0; i < nDOF; ++i) { |
---|
| 2979 | double xFactor = 2.0/(double)(nChan - 1); |
---|
| 2980 | std::vector<double> xs; |
---|
| 2981 | xs.clear(); |
---|
| 2982 | for (int j = 0; j < nChan; ++j) { |
---|
| 2983 | xs.push_back(getChebyshevPolynomial(i, xFactor*(double)j-1.0)); |
---|
| 2984 | } |
---|
| 2985 | xArray.push_back(xs); |
---|
| 2986 | } |
---|
| 2987 | |
---|
| 2988 | std::vector<double> z1, r1, residual; |
---|
| 2989 | for (int i = 0; i < nChan; ++i) { |
---|
| 2990 | z1.push_back((double)data[i]); |
---|
| 2991 | r1.push_back(0.0); |
---|
| 2992 | residual.push_back(0.0); |
---|
| 2993 | } |
---|
| 2994 | |
---|
| 2995 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
| 2996 | // xMatrix : horizontal concatenation of |
---|
| 2997 | // the least-sq. matrix (left) and an |
---|
| 2998 | // identity matrix (right). |
---|
| 2999 | // the right part is used to calculate the inverse matrix of the left part. |
---|
| 3000 | double xMatrix[nDOF][2*nDOF]; |
---|
| 3001 | double zMatrix[nDOF]; |
---|
| 3002 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3003 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
| 3004 | xMatrix[i][j] = 0.0; |
---|
| 3005 | } |
---|
| 3006 | xMatrix[i][nDOF+i] = 1.0; |
---|
| 3007 | zMatrix[i] = 0.0; |
---|
| 3008 | } |
---|
| 3009 | |
---|
| 3010 | int nUseData = 0; |
---|
| 3011 | for (int k = 0; k < nChan; ++k) { |
---|
| 3012 | if (maskArray[k] == 0) continue; |
---|
| 3013 | |
---|
| 3014 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3015 | for (int j = i; j < nDOF; ++j) { |
---|
| 3016 | xMatrix[i][j] += xArray[i][k] * xArray[j][k]; |
---|
| 3017 | } |
---|
| 3018 | zMatrix[i] += z1[k] * xArray[i][k]; |
---|
| 3019 | } |
---|
| 3020 | |
---|
| 3021 | nUseData++; |
---|
| 3022 | } |
---|
| 3023 | |
---|
| 3024 | if (nUseData < 1) { |
---|
| 3025 | throw(AipsError("all channels clipped or masked. can't execute fitting anymore.")); |
---|
| 3026 | } |
---|
| 3027 | |
---|
| 3028 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3029 | for (int j = 0; j < i; ++j) { |
---|
| 3030 | xMatrix[i][j] = xMatrix[j][i]; |
---|
| 3031 | } |
---|
| 3032 | } |
---|
| 3033 | |
---|
| 3034 | std::vector<double> invDiag; |
---|
| 3035 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3036 | invDiag.push_back(1.0/xMatrix[i][i]); |
---|
| 3037 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3038 | xMatrix[i][j] *= invDiag[i]; |
---|
| 3039 | } |
---|
| 3040 | } |
---|
| 3041 | |
---|
| 3042 | for (int k = 0; k < nDOF; ++k) { |
---|
| 3043 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3044 | if (i != k) { |
---|
| 3045 | double factor1 = xMatrix[k][k]; |
---|
| 3046 | double factor2 = xMatrix[i][k]; |
---|
| 3047 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 3048 | xMatrix[i][j] *= factor1; |
---|
| 3049 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
| 3050 | xMatrix[i][j] /= factor1; |
---|
| 3051 | } |
---|
| 3052 | } |
---|
| 3053 | } |
---|
| 3054 | double xDiag = xMatrix[k][k]; |
---|
| 3055 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 3056 | xMatrix[k][j] /= xDiag; |
---|
| 3057 | } |
---|
| 3058 | } |
---|
| 3059 | |
---|
| 3060 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3061 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3062 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
| 3063 | } |
---|
| 3064 | } |
---|
| 3065 | //compute a vector y which consists of the coefficients of the sinusoids forming the |
---|
| 3066 | //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine |
---|
| 3067 | //and cosine functions, respectively. |
---|
| 3068 | std::vector<double> y; |
---|
| 3069 | params.clear(); |
---|
| 3070 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3071 | y.push_back(0.0); |
---|
| 3072 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3073 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
| 3074 | } |
---|
| 3075 | params.push_back(y[i]); |
---|
| 3076 | } |
---|
| 3077 | |
---|
| 3078 | for (int i = 0; i < nChan; ++i) { |
---|
| 3079 | r1[i] = y[0]; |
---|
| 3080 | for (int j = 1; j < nDOF; ++j) { |
---|
| 3081 | r1[i] += y[j]*xArray[j][i]; |
---|
| 3082 | } |
---|
| 3083 | residual[i] = z1[i] - r1[i]; |
---|
| 3084 | } |
---|
| 3085 | |
---|
[2737] | 3086 | double stdDev = 0.0; |
---|
| 3087 | for (int i = 0; i < nChan; ++i) { |
---|
| 3088 | stdDev += residual[i]*residual[i]*(double)maskArray[i]; |
---|
| 3089 | } |
---|
| 3090 | stdDev = sqrt(stdDev/(double)nData); |
---|
| 3091 | rms = (float)stdDev; |
---|
| 3092 | |
---|
[2645] | 3093 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
| 3094 | break; |
---|
| 3095 | } else { |
---|
[2737] | 3096 | |
---|
[2645] | 3097 | double thres = stdDev * thresClip; |
---|
| 3098 | int newNData = 0; |
---|
| 3099 | for (int i = 0; i < nChan; ++i) { |
---|
| 3100 | if (abs(residual[i]) >= thres) { |
---|
| 3101 | maskArray[i] = 0; |
---|
[2737] | 3102 | finalMask[i] = false; |
---|
[2645] | 3103 | } |
---|
| 3104 | if (maskArray[i] > 0) { |
---|
| 3105 | newNData++; |
---|
| 3106 | } |
---|
| 3107 | } |
---|
| 3108 | if (newNData == nData) { |
---|
| 3109 | break; //no more flag to add. iteration stops. |
---|
| 3110 | } else { |
---|
| 3111 | nData = newNData; |
---|
| 3112 | } |
---|
[2737] | 3113 | |
---|
[2645] | 3114 | } |
---|
| 3115 | } |
---|
| 3116 | |
---|
| 3117 | nClipped = initNData - nData; |
---|
| 3118 | |
---|
| 3119 | std::vector<float> result; |
---|
| 3120 | if (getResidual) { |
---|
| 3121 | for (int i = 0; i < nChan; ++i) { |
---|
| 3122 | result.push_back((float)residual[i]); |
---|
| 3123 | } |
---|
| 3124 | } else { |
---|
| 3125 | for (int i = 0; i < nChan; ++i) { |
---|
| 3126 | result.push_back((float)r1[i]); |
---|
| 3127 | } |
---|
| 3128 | } |
---|
| 3129 | |
---|
| 3130 | return result; |
---|
| 3131 | } |
---|
| 3132 | |
---|
[2189] | 3133 | void Scantable::cubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2081] | 3134 | { |
---|
[2641] | 3135 | /************* |
---|
[2591] | 3136 | double totTimeStart, totTimeEnd, blTimeStart, blTimeEnd, ioTimeStart, ioTimeEnd, msTimeStart, msTimeEnd, seTimeStart, seTimeEnd, otTimeStart, otTimeEnd, prTimeStart, prTimeEnd; |
---|
| 3137 | double elapseMs = 0.0; |
---|
| 3138 | double elapseSe = 0.0; |
---|
| 3139 | double elapseOt = 0.0; |
---|
| 3140 | double elapsePr = 0.0; |
---|
| 3141 | double elapseBl = 0.0; |
---|
| 3142 | double elapseIo = 0.0; |
---|
| 3143 | totTimeStart = mathutil::gettimeofday_sec(); |
---|
[2641] | 3144 | *************/ |
---|
[2591] | 3145 | |
---|
[2193] | 3146 | try { |
---|
| 3147 | ofstream ofs; |
---|
| 3148 | String coordInfo = ""; |
---|
| 3149 | bool hasSameNchan = true; |
---|
| 3150 | bool outTextFile = false; |
---|
[2641] | 3151 | bool csvFormat = false; |
---|
[2012] | 3152 | |
---|
[2193] | 3153 | if (blfile != "") { |
---|
[2641] | 3154 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
| 3155 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
[2193] | 3156 | if (ofs) outTextFile = true; |
---|
| 3157 | } |
---|
[2012] | 3158 | |
---|
[2193] | 3159 | if (outLogger || outTextFile) { |
---|
| 3160 | coordInfo = getCoordInfo()[0]; |
---|
| 3161 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 3162 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 3163 | } |
---|
[2012] | 3164 | |
---|
[2193] | 3165 | //Fitter fitter = Fitter(); |
---|
| 3166 | //fitter.setExpression("cspline", nPiece); |
---|
| 3167 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2012] | 3168 | |
---|
[2193] | 3169 | bool showProgress; |
---|
| 3170 | int minNRow; |
---|
| 3171 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2012] | 3172 | |
---|
[2344] | 3173 | int nRow = nrow(); |
---|
| 3174 | std::vector<bool> chanMask; |
---|
| 3175 | |
---|
| 3176 | //-------------------------------- |
---|
[2193] | 3177 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2641] | 3178 | /****************** |
---|
[2591] | 3179 | ioTimeStart = mathutil::gettimeofday_sec(); |
---|
[2641] | 3180 | **/ |
---|
[2591] | 3181 | std::vector<float> sp = getSpectrum(whichrow); |
---|
[2641] | 3182 | /** |
---|
[2591] | 3183 | ioTimeEnd = mathutil::gettimeofday_sec(); |
---|
| 3184 | elapseIo += (double)(ioTimeEnd - ioTimeStart); |
---|
| 3185 | msTimeStart = mathutil::gettimeofday_sec(); |
---|
[2641] | 3186 | ******************/ |
---|
[2591] | 3187 | |
---|
[2193] | 3188 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
[2591] | 3189 | |
---|
[2641] | 3190 | /** |
---|
[2591] | 3191 | msTimeEnd = mathutil::gettimeofday_sec(); |
---|
| 3192 | elapseMs += (double)(msTimeEnd - msTimeStart); |
---|
| 3193 | blTimeStart = mathutil::gettimeofday_sec(); |
---|
[2641] | 3194 | **/ |
---|
[2591] | 3195 | |
---|
[2193] | 3196 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 3197 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
[2344] | 3198 | std::vector<int> pieceEdges(nPiece+1); |
---|
| 3199 | std::vector<float> params(nPiece*4); |
---|
[2193] | 3200 | int nClipped = 0; |
---|
[2591] | 3201 | std::vector<float> res = doCubicSplineFitting(sp, chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual); |
---|
| 3202 | |
---|
[2641] | 3203 | /** |
---|
[2591] | 3204 | blTimeEnd = mathutil::gettimeofday_sec(); |
---|
| 3205 | elapseBl += (double)(blTimeEnd - blTimeStart); |
---|
| 3206 | seTimeStart = mathutil::gettimeofday_sec(); |
---|
[2641] | 3207 | **/ |
---|
[2591] | 3208 | |
---|
| 3209 | |
---|
[2193] | 3210 | setSpectrum(res, whichrow); |
---|
| 3211 | // |
---|
[2012] | 3212 | |
---|
[2641] | 3213 | /** |
---|
[2591] | 3214 | seTimeEnd = mathutil::gettimeofday_sec(); |
---|
| 3215 | elapseSe += (double)(seTimeEnd - seTimeStart); |
---|
| 3216 | otTimeStart = mathutil::gettimeofday_sec(); |
---|
[2641] | 3217 | **/ |
---|
[2591] | 3218 | |
---|
[2641] | 3219 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "cubicSplineBaseline()", pieceEdges, params, nClipped); |
---|
[2591] | 3220 | |
---|
[2641] | 3221 | /** |
---|
[2591] | 3222 | otTimeEnd = mathutil::gettimeofday_sec(); |
---|
| 3223 | elapseOt += (double)(otTimeEnd - otTimeStart); |
---|
| 3224 | prTimeStart = mathutil::gettimeofday_sec(); |
---|
[2641] | 3225 | **/ |
---|
[2591] | 3226 | |
---|
[2193] | 3227 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[2591] | 3228 | |
---|
[2641] | 3229 | /****************** |
---|
[2591] | 3230 | prTimeEnd = mathutil::gettimeofday_sec(); |
---|
| 3231 | elapsePr += (double)(prTimeEnd - prTimeStart); |
---|
[2641] | 3232 | ******************/ |
---|
[2193] | 3233 | } |
---|
[2344] | 3234 | //-------------------------------- |
---|
| 3235 | |
---|
[2193] | 3236 | if (outTextFile) ofs.close(); |
---|
| 3237 | |
---|
| 3238 | } catch (...) { |
---|
| 3239 | throw; |
---|
[2012] | 3240 | } |
---|
[2641] | 3241 | /*************** |
---|
[2591] | 3242 | totTimeEnd = mathutil::gettimeofday_sec(); |
---|
| 3243 | std::cout << "io : " << elapseIo << " (sec.)" << endl; |
---|
| 3244 | std::cout << "ms : " << elapseMs << " (sec.)" << endl; |
---|
| 3245 | std::cout << "bl : " << elapseBl << " (sec.)" << endl; |
---|
| 3246 | std::cout << "se : " << elapseSe << " (sec.)" << endl; |
---|
| 3247 | std::cout << "ot : " << elapseOt << " (sec.)" << endl; |
---|
| 3248 | std::cout << "pr : " << elapsePr << " (sec.)" << endl; |
---|
| 3249 | std::cout << "total : " << (double)(totTimeEnd - totTimeStart) << " (sec.)" << endl; |
---|
[2641] | 3250 | ***************/ |
---|
[2012] | 3251 | } |
---|
| 3252 | |
---|
[2189] | 3253 | void Scantable::autoCubicSplineBaseline(const std::vector<bool>& mask, int nPiece, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2012] | 3254 | { |
---|
[2193] | 3255 | try { |
---|
| 3256 | ofstream ofs; |
---|
| 3257 | String coordInfo = ""; |
---|
| 3258 | bool hasSameNchan = true; |
---|
| 3259 | bool outTextFile = false; |
---|
[2641] | 3260 | bool csvFormat = false; |
---|
[2012] | 3261 | |
---|
[2193] | 3262 | if (blfile != "") { |
---|
[2641] | 3263 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
| 3264 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
[2193] | 3265 | if (ofs) outTextFile = true; |
---|
| 3266 | } |
---|
[2012] | 3267 | |
---|
[2193] | 3268 | if (outLogger || outTextFile) { |
---|
| 3269 | coordInfo = getCoordInfo()[0]; |
---|
| 3270 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 3271 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 3272 | } |
---|
[2012] | 3273 | |
---|
[2193] | 3274 | //Fitter fitter = Fitter(); |
---|
| 3275 | //fitter.setExpression("cspline", nPiece); |
---|
| 3276 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2012] | 3277 | |
---|
[2193] | 3278 | int nRow = nrow(); |
---|
| 3279 | std::vector<bool> chanMask; |
---|
| 3280 | int minEdgeSize = getIFNos().size()*2; |
---|
| 3281 | STLineFinder lineFinder = STLineFinder(); |
---|
| 3282 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
[2012] | 3283 | |
---|
[2193] | 3284 | bool showProgress; |
---|
| 3285 | int minNRow; |
---|
| 3286 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2189] | 3287 | |
---|
[2193] | 3288 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2591] | 3289 | std::vector<float> sp = getSpectrum(whichrow); |
---|
[2012] | 3290 | |
---|
[2193] | 3291 | //------------------------------------------------------- |
---|
| 3292 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
| 3293 | //------------------------------------------------------- |
---|
| 3294 | int edgeSize = edge.size(); |
---|
| 3295 | std::vector<int> currentEdge; |
---|
| 3296 | if (edgeSize >= 2) { |
---|
| 3297 | int idx = 0; |
---|
| 3298 | if (edgeSize > 2) { |
---|
| 3299 | if (edgeSize < minEdgeSize) { |
---|
| 3300 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 3301 | } |
---|
| 3302 | idx = 2 * getIF(whichrow); |
---|
[2012] | 3303 | } |
---|
[2193] | 3304 | currentEdge.push_back(edge[idx]); |
---|
| 3305 | currentEdge.push_back(edge[idx+1]); |
---|
| 3306 | } else { |
---|
| 3307 | throw(AipsError("Wrong length of edge element")); |
---|
[2012] | 3308 | } |
---|
[2641] | 3309 | //lineFinder.setData(getSpectrum(whichrow)); |
---|
| 3310 | lineFinder.setData(sp); |
---|
[2193] | 3311 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
| 3312 | chanMask = lineFinder.getMask(); |
---|
| 3313 | //------------------------------------------------------- |
---|
| 3314 | |
---|
| 3315 | |
---|
| 3316 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 3317 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
[2344] | 3318 | std::vector<int> pieceEdges(nPiece+1); |
---|
| 3319 | std::vector<float> params(nPiece*4); |
---|
[2193] | 3320 | int nClipped = 0; |
---|
[2591] | 3321 | std::vector<float> res = doCubicSplineFitting(sp, chanMask, nPiece, pieceEdges, params, nClipped, thresClip, nIterClip, getResidual); |
---|
[2193] | 3322 | setSpectrum(res, whichrow); |
---|
| 3323 | // |
---|
| 3324 | |
---|
[2641] | 3325 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoCubicSplineBaseline()", pieceEdges, params, nClipped); |
---|
[2193] | 3326 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[1907] | 3327 | } |
---|
[2012] | 3328 | |
---|
[2193] | 3329 | if (outTextFile) ofs.close(); |
---|
[2012] | 3330 | |
---|
[2193] | 3331 | } catch (...) { |
---|
| 3332 | throw; |
---|
[2012] | 3333 | } |
---|
[1730] | 3334 | } |
---|
[1907] | 3335 | |
---|
[2193] | 3336 | std::vector<float> Scantable::doCubicSplineFitting(const std::vector<float>& data, const std::vector<bool>& mask, int nPiece, std::vector<int>& idxEdge, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual) |
---|
[2081] | 3337 | { |
---|
| 3338 | if (data.size() != mask.size()) { |
---|
| 3339 | throw(AipsError("data and mask sizes are not identical")); |
---|
| 3340 | } |
---|
[2012] | 3341 | if (nPiece < 1) { |
---|
[2094] | 3342 | throw(AipsError("number of the sections must be one or more")); |
---|
[2012] | 3343 | } |
---|
| 3344 | |
---|
| 3345 | int nChan = data.size(); |
---|
[2344] | 3346 | std::vector<int> maskArray(nChan); |
---|
| 3347 | std::vector<int> x(nChan); |
---|
| 3348 | int j = 0; |
---|
[2012] | 3349 | for (int i = 0; i < nChan; ++i) { |
---|
[2344] | 3350 | maskArray[i] = mask[i] ? 1 : 0; |
---|
[2012] | 3351 | if (mask[i]) { |
---|
[2344] | 3352 | x[j] = i; |
---|
| 3353 | j++; |
---|
[2012] | 3354 | } |
---|
| 3355 | } |
---|
[2344] | 3356 | int initNData = j; |
---|
[2012] | 3357 | |
---|
[2193] | 3358 | if (initNData < nPiece) { |
---|
| 3359 | throw(AipsError("too few non-flagged channels")); |
---|
| 3360 | } |
---|
[2081] | 3361 | |
---|
| 3362 | int nElement = (int)(floor(floor((double)(initNData/nPiece))+0.5)); |
---|
[2344] | 3363 | std::vector<double> invEdge(nPiece-1); |
---|
| 3364 | idxEdge[0] = x[0]; |
---|
[2012] | 3365 | for (int i = 1; i < nPiece; ++i) { |
---|
[2047] | 3366 | int valX = x[nElement*i]; |
---|
[2344] | 3367 | idxEdge[i] = valX; |
---|
| 3368 | invEdge[i-1] = 1.0/(double)valX; |
---|
[2012] | 3369 | } |
---|
[2344] | 3370 | idxEdge[nPiece] = x[initNData-1]+1; |
---|
[2064] | 3371 | |
---|
[2081] | 3372 | int nData = initNData; |
---|
| 3373 | int nDOF = nPiece + 3; //number of parameters to solve, namely, 4+(nPiece-1). |
---|
| 3374 | |
---|
[2344] | 3375 | std::vector<double> x1(nChan), x2(nChan), x3(nChan); |
---|
| 3376 | std::vector<double> z1(nChan), x1z1(nChan), x2z1(nChan), x3z1(nChan); |
---|
| 3377 | std::vector<double> r1(nChan), residual(nChan); |
---|
[2012] | 3378 | for (int i = 0; i < nChan; ++i) { |
---|
[2064] | 3379 | double di = (double)i; |
---|
| 3380 | double dD = (double)data[i]; |
---|
[2344] | 3381 | x1[i] = di; |
---|
| 3382 | x2[i] = di*di; |
---|
| 3383 | x3[i] = di*di*di; |
---|
| 3384 | z1[i] = dD; |
---|
| 3385 | x1z1[i] = dD*di; |
---|
| 3386 | x2z1[i] = dD*di*di; |
---|
| 3387 | x3z1[i] = dD*di*di*di; |
---|
| 3388 | r1[i] = 0.0; |
---|
| 3389 | residual[i] = 0.0; |
---|
[2012] | 3390 | } |
---|
| 3391 | |
---|
| 3392 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
[2064] | 3393 | // xMatrix : horizontal concatenation of |
---|
| 3394 | // the least-sq. matrix (left) and an |
---|
| 3395 | // identity matrix (right). |
---|
| 3396 | // the right part is used to calculate the inverse matrix of the left part. |
---|
[2012] | 3397 | double xMatrix[nDOF][2*nDOF]; |
---|
| 3398 | double zMatrix[nDOF]; |
---|
| 3399 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3400 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
| 3401 | xMatrix[i][j] = 0.0; |
---|
| 3402 | } |
---|
| 3403 | xMatrix[i][nDOF+i] = 1.0; |
---|
| 3404 | zMatrix[i] = 0.0; |
---|
| 3405 | } |
---|
| 3406 | |
---|
| 3407 | for (int n = 0; n < nPiece; ++n) { |
---|
[2193] | 3408 | int nUseDataInPiece = 0; |
---|
[2064] | 3409 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) { |
---|
| 3410 | |
---|
[2012] | 3411 | if (maskArray[i] == 0) continue; |
---|
[2064] | 3412 | |
---|
[2012] | 3413 | xMatrix[0][0] += 1.0; |
---|
[2064] | 3414 | xMatrix[0][1] += x1[i]; |
---|
| 3415 | xMatrix[0][2] += x2[i]; |
---|
| 3416 | xMatrix[0][3] += x3[i]; |
---|
| 3417 | xMatrix[1][1] += x2[i]; |
---|
| 3418 | xMatrix[1][2] += x3[i]; |
---|
| 3419 | xMatrix[1][3] += x2[i]*x2[i]; |
---|
| 3420 | xMatrix[2][2] += x2[i]*x2[i]; |
---|
| 3421 | xMatrix[2][3] += x3[i]*x2[i]; |
---|
| 3422 | xMatrix[3][3] += x3[i]*x3[i]; |
---|
[2012] | 3423 | zMatrix[0] += z1[i]; |
---|
[2064] | 3424 | zMatrix[1] += x1z1[i]; |
---|
| 3425 | zMatrix[2] += x2z1[i]; |
---|
| 3426 | zMatrix[3] += x3z1[i]; |
---|
| 3427 | |
---|
[2012] | 3428 | for (int j = 0; j < n; ++j) { |
---|
[2064] | 3429 | double q = 1.0 - x1[i]*invEdge[j]; |
---|
[2012] | 3430 | q = q*q*q; |
---|
| 3431 | xMatrix[0][j+4] += q; |
---|
[2064] | 3432 | xMatrix[1][j+4] += q*x1[i]; |
---|
| 3433 | xMatrix[2][j+4] += q*x2[i]; |
---|
| 3434 | xMatrix[3][j+4] += q*x3[i]; |
---|
[2012] | 3435 | for (int k = 0; k < j; ++k) { |
---|
[2064] | 3436 | double r = 1.0 - x1[i]*invEdge[k]; |
---|
[2012] | 3437 | r = r*r*r; |
---|
| 3438 | xMatrix[k+4][j+4] += r*q; |
---|
| 3439 | } |
---|
| 3440 | xMatrix[j+4][j+4] += q*q; |
---|
| 3441 | zMatrix[j+4] += q*z1[i]; |
---|
| 3442 | } |
---|
[2064] | 3443 | |
---|
[2193] | 3444 | nUseDataInPiece++; |
---|
[2012] | 3445 | } |
---|
[2193] | 3446 | |
---|
| 3447 | if (nUseDataInPiece < 1) { |
---|
| 3448 | std::vector<string> suffixOfPieceNumber(4); |
---|
| 3449 | suffixOfPieceNumber[0] = "th"; |
---|
| 3450 | suffixOfPieceNumber[1] = "st"; |
---|
| 3451 | suffixOfPieceNumber[2] = "nd"; |
---|
| 3452 | suffixOfPieceNumber[3] = "rd"; |
---|
| 3453 | int idxNoDataPiece = (n % 10 <= 3) ? n : 0; |
---|
| 3454 | ostringstream oss; |
---|
| 3455 | oss << "all channels clipped or masked in " << n << suffixOfPieceNumber[idxNoDataPiece]; |
---|
| 3456 | oss << " piece of the spectrum. can't execute fitting anymore."; |
---|
| 3457 | throw(AipsError(String(oss))); |
---|
| 3458 | } |
---|
[2012] | 3459 | } |
---|
| 3460 | |
---|
| 3461 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3462 | for (int j = 0; j < i; ++j) { |
---|
| 3463 | xMatrix[i][j] = xMatrix[j][i]; |
---|
| 3464 | } |
---|
| 3465 | } |
---|
| 3466 | |
---|
[2344] | 3467 | std::vector<double> invDiag(nDOF); |
---|
[2012] | 3468 | for (int i = 0; i < nDOF; ++i) { |
---|
[2344] | 3469 | invDiag[i] = 1.0/xMatrix[i][i]; |
---|
[2012] | 3470 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3471 | xMatrix[i][j] *= invDiag[i]; |
---|
| 3472 | } |
---|
| 3473 | } |
---|
| 3474 | |
---|
| 3475 | for (int k = 0; k < nDOF; ++k) { |
---|
| 3476 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3477 | if (i != k) { |
---|
| 3478 | double factor1 = xMatrix[k][k]; |
---|
| 3479 | double factor2 = xMatrix[i][k]; |
---|
| 3480 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 3481 | xMatrix[i][j] *= factor1; |
---|
| 3482 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
| 3483 | xMatrix[i][j] /= factor1; |
---|
| 3484 | } |
---|
| 3485 | } |
---|
| 3486 | } |
---|
| 3487 | double xDiag = xMatrix[k][k]; |
---|
| 3488 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 3489 | xMatrix[k][j] /= xDiag; |
---|
| 3490 | } |
---|
| 3491 | } |
---|
| 3492 | |
---|
| 3493 | for (int i = 0; i < nDOF; ++i) { |
---|
| 3494 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3495 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
| 3496 | } |
---|
| 3497 | } |
---|
| 3498 | //compute a vector y which consists of the coefficients of the best-fit spline curves |
---|
| 3499 | //(a0,a1,a2,a3(,b3,c3,...)), namely, the ones for the leftmost piece and the ones of |
---|
| 3500 | //cubic terms for the other pieces (in case nPiece>1). |
---|
[2344] | 3501 | std::vector<double> y(nDOF); |
---|
[2012] | 3502 | for (int i = 0; i < nDOF; ++i) { |
---|
[2344] | 3503 | y[i] = 0.0; |
---|
[2012] | 3504 | for (int j = 0; j < nDOF; ++j) { |
---|
| 3505 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
| 3506 | } |
---|
| 3507 | } |
---|
| 3508 | |
---|
| 3509 | double a0 = y[0]; |
---|
| 3510 | double a1 = y[1]; |
---|
| 3511 | double a2 = y[2]; |
---|
| 3512 | double a3 = y[3]; |
---|
| 3513 | |
---|
[2344] | 3514 | int j = 0; |
---|
[2012] | 3515 | for (int n = 0; n < nPiece; ++n) { |
---|
[2064] | 3516 | for (int i = idxEdge[n]; i < idxEdge[n+1]; ++i) { |
---|
| 3517 | r1[i] = a0 + a1*x1[i] + a2*x2[i] + a3*x3[i]; |
---|
[2012] | 3518 | } |
---|
[2344] | 3519 | params[j] = a0; |
---|
| 3520 | params[j+1] = a1; |
---|
| 3521 | params[j+2] = a2; |
---|
| 3522 | params[j+3] = a3; |
---|
| 3523 | j += 4; |
---|
[2012] | 3524 | |
---|
| 3525 | if (n == nPiece-1) break; |
---|
| 3526 | |
---|
| 3527 | double d = y[4+n]; |
---|
[2064] | 3528 | double iE = invEdge[n]; |
---|
| 3529 | a0 += d; |
---|
| 3530 | a1 -= 3.0*d*iE; |
---|
| 3531 | a2 += 3.0*d*iE*iE; |
---|
| 3532 | a3 -= d*iE*iE*iE; |
---|
[2012] | 3533 | } |
---|
| 3534 | |
---|
[2344] | 3535 | //subtract constant value for masked regions at the edge of spectrum |
---|
| 3536 | if (idxEdge[0] > 0) { |
---|
| 3537 | int n = idxEdge[0]; |
---|
| 3538 | for (int i = 0; i < idxEdge[0]; ++i) { |
---|
| 3539 | //--cubic extrapolate-- |
---|
| 3540 | //r1[i] = params[0] + params[1]*x1[i] + params[2]*x2[i] + params[3]*x3[i]; |
---|
| 3541 | //--linear extrapolate-- |
---|
| 3542 | //r1[i] = (r1[n+1] - r1[n])/(x1[n+1] - x1[n])*(x1[i] - x1[n]) + r1[n]; |
---|
| 3543 | //--constant-- |
---|
| 3544 | r1[i] = r1[n]; |
---|
| 3545 | } |
---|
| 3546 | } |
---|
| 3547 | if (idxEdge[nPiece] < nChan) { |
---|
| 3548 | int n = idxEdge[nPiece]-1; |
---|
| 3549 | for (int i = idxEdge[nPiece]; i < nChan; ++i) { |
---|
| 3550 | //--cubic extrapolate-- |
---|
| 3551 | //int m = 4*(nPiece-1); |
---|
| 3552 | //r1[i] = params[m] + params[m+1]*x1[i] + params[m+2]*x2[i] + params[m+3]*x3[i]; |
---|
| 3553 | //--linear extrapolate-- |
---|
| 3554 | //r1[i] = (r1[n-1] - r1[n])/(x1[n-1] - x1[n])*(x1[i] - x1[n]) + r1[n]; |
---|
| 3555 | //--constant-- |
---|
| 3556 | r1[i] = r1[n]; |
---|
| 3557 | } |
---|
| 3558 | } |
---|
| 3559 | |
---|
| 3560 | for (int i = 0; i < nChan; ++i) { |
---|
| 3561 | residual[i] = z1[i] - r1[i]; |
---|
| 3562 | } |
---|
| 3563 | |
---|
[2012] | 3564 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
| 3565 | break; |
---|
| 3566 | } else { |
---|
| 3567 | double stdDev = 0.0; |
---|
| 3568 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3569 | stdDev += residual[i]*residual[i]*(double)maskArray[i]; |
---|
[2012] | 3570 | } |
---|
| 3571 | stdDev = sqrt(stdDev/(double)nData); |
---|
| 3572 | |
---|
| 3573 | double thres = stdDev * thresClip; |
---|
| 3574 | int newNData = 0; |
---|
| 3575 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3576 | if (abs(residual[i]) >= thres) { |
---|
[2012] | 3577 | maskArray[i] = 0; |
---|
| 3578 | } |
---|
| 3579 | if (maskArray[i] > 0) { |
---|
| 3580 | newNData++; |
---|
| 3581 | } |
---|
| 3582 | } |
---|
[2081] | 3583 | if (newNData == nData) { |
---|
[2064] | 3584 | break; //no more flag to add. iteration stops. |
---|
[2012] | 3585 | } else { |
---|
[2081] | 3586 | nData = newNData; |
---|
[2012] | 3587 | } |
---|
| 3588 | } |
---|
| 3589 | } |
---|
| 3590 | |
---|
[2193] | 3591 | nClipped = initNData - nData; |
---|
| 3592 | |
---|
[2344] | 3593 | std::vector<float> result(nChan); |
---|
[2058] | 3594 | if (getResidual) { |
---|
| 3595 | for (int i = 0; i < nChan; ++i) { |
---|
[2344] | 3596 | result[i] = (float)residual[i]; |
---|
[2058] | 3597 | } |
---|
| 3598 | } else { |
---|
| 3599 | for (int i = 0; i < nChan; ++i) { |
---|
[2344] | 3600 | result[i] = (float)r1[i]; |
---|
[2058] | 3601 | } |
---|
[2012] | 3602 | } |
---|
| 3603 | |
---|
[2058] | 3604 | return result; |
---|
[2012] | 3605 | } |
---|
| 3606 | |
---|
[2344] | 3607 | void Scantable::selectWaveNumbers(const int whichrow, const std::vector<bool>& chanMask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves) |
---|
[2081] | 3608 | { |
---|
[2186] | 3609 | nWaves.clear(); |
---|
| 3610 | |
---|
| 3611 | if (applyFFT) { |
---|
| 3612 | string fftThAttr; |
---|
| 3613 | float fftThSigma; |
---|
| 3614 | int fftThTop; |
---|
| 3615 | parseThresholdExpression(fftThresh, fftThAttr, fftThSigma, fftThTop); |
---|
| 3616 | doSelectWaveNumbers(whichrow, chanMask, fftMethod, fftThSigma, fftThTop, fftThAttr, nWaves); |
---|
| 3617 | } |
---|
| 3618 | |
---|
[2411] | 3619 | addAuxWaveNumbers(whichrow, addNWaves, rejectNWaves, nWaves); |
---|
[2186] | 3620 | } |
---|
| 3621 | |
---|
| 3622 | void Scantable::parseThresholdExpression(const std::string& fftThresh, std::string& fftThAttr, float& fftThSigma, int& fftThTop) |
---|
| 3623 | { |
---|
| 3624 | uInt idxSigma = fftThresh.find("sigma"); |
---|
| 3625 | uInt idxTop = fftThresh.find("top"); |
---|
| 3626 | |
---|
| 3627 | if (idxSigma == fftThresh.size() - 5) { |
---|
| 3628 | std::istringstream is(fftThresh.substr(0, fftThresh.size() - 5)); |
---|
| 3629 | is >> fftThSigma; |
---|
| 3630 | fftThAttr = "sigma"; |
---|
| 3631 | } else if (idxTop == 0) { |
---|
| 3632 | std::istringstream is(fftThresh.substr(3)); |
---|
| 3633 | is >> fftThTop; |
---|
| 3634 | fftThAttr = "top"; |
---|
| 3635 | } else { |
---|
| 3636 | bool isNumber = true; |
---|
| 3637 | for (uInt i = 0; i < fftThresh.size()-1; ++i) { |
---|
| 3638 | char ch = (fftThresh.substr(i, 1).c_str())[0]; |
---|
| 3639 | if (!(isdigit(ch) || (fftThresh.substr(i, 1) == "."))) { |
---|
| 3640 | isNumber = false; |
---|
| 3641 | break; |
---|
| 3642 | } |
---|
| 3643 | } |
---|
| 3644 | if (isNumber) { |
---|
| 3645 | std::istringstream is(fftThresh); |
---|
| 3646 | is >> fftThSigma; |
---|
| 3647 | fftThAttr = "sigma"; |
---|
| 3648 | } else { |
---|
| 3649 | throw(AipsError("fftthresh has a wrong value")); |
---|
| 3650 | } |
---|
| 3651 | } |
---|
| 3652 | } |
---|
| 3653 | |
---|
| 3654 | void Scantable::doSelectWaveNumbers(const int whichrow, const std::vector<bool>& chanMask, const std::string& fftMethod, const float fftThSigma, const int fftThTop, const std::string& fftThAttr, std::vector<int>& nWaves) |
---|
| 3655 | { |
---|
| 3656 | std::vector<float> fspec; |
---|
| 3657 | if (fftMethod == "fft") { |
---|
| 3658 | fspec = execFFT(whichrow, chanMask, false, true); |
---|
| 3659 | //} else if (fftMethod == "lsp") { |
---|
| 3660 | // fspec = lombScarglePeriodogram(whichrow); |
---|
| 3661 | } |
---|
| 3662 | |
---|
| 3663 | if (fftThAttr == "sigma") { |
---|
| 3664 | float mean = 0.0; |
---|
| 3665 | float mean2 = 0.0; |
---|
| 3666 | for (uInt i = 0; i < fspec.size(); ++i) { |
---|
| 3667 | mean += fspec[i]; |
---|
| 3668 | mean2 += fspec[i]*fspec[i]; |
---|
| 3669 | } |
---|
| 3670 | mean /= float(fspec.size()); |
---|
| 3671 | mean2 /= float(fspec.size()); |
---|
| 3672 | float thres = mean + fftThSigma * float(sqrt(mean2 - mean*mean)); |
---|
| 3673 | |
---|
| 3674 | for (uInt i = 0; i < fspec.size(); ++i) { |
---|
| 3675 | if (fspec[i] >= thres) { |
---|
| 3676 | nWaves.push_back(i); |
---|
| 3677 | } |
---|
| 3678 | } |
---|
| 3679 | |
---|
| 3680 | } else if (fftThAttr == "top") { |
---|
| 3681 | for (int i = 0; i < fftThTop; ++i) { |
---|
| 3682 | float max = 0.0; |
---|
| 3683 | int maxIdx = 0; |
---|
| 3684 | for (uInt j = 0; j < fspec.size(); ++j) { |
---|
| 3685 | if (fspec[j] > max) { |
---|
| 3686 | max = fspec[j]; |
---|
| 3687 | maxIdx = j; |
---|
| 3688 | } |
---|
| 3689 | } |
---|
| 3690 | nWaves.push_back(maxIdx); |
---|
| 3691 | fspec[maxIdx] = 0.0; |
---|
| 3692 | } |
---|
| 3693 | |
---|
| 3694 | } |
---|
| 3695 | |
---|
| 3696 | if (nWaves.size() > 1) { |
---|
| 3697 | sort(nWaves.begin(), nWaves.end()); |
---|
| 3698 | } |
---|
| 3699 | } |
---|
| 3700 | |
---|
[2411] | 3701 | void Scantable::addAuxWaveNumbers(const int whichrow, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, std::vector<int>& nWaves) |
---|
[2186] | 3702 | { |
---|
[2411] | 3703 | std::vector<int> tempAddNWaves, tempRejectNWaves; |
---|
[2186] | 3704 | for (uInt i = 0; i < addNWaves.size(); ++i) { |
---|
[2411] | 3705 | tempAddNWaves.push_back(addNWaves[i]); |
---|
| 3706 | } |
---|
| 3707 | if ((tempAddNWaves.size() == 2) && (tempAddNWaves[1] == -999)) { |
---|
| 3708 | setWaveNumberListUptoNyquistFreq(whichrow, tempAddNWaves); |
---|
| 3709 | } |
---|
| 3710 | |
---|
| 3711 | for (uInt i = 0; i < rejectNWaves.size(); ++i) { |
---|
| 3712 | tempRejectNWaves.push_back(rejectNWaves[i]); |
---|
| 3713 | } |
---|
| 3714 | if ((tempRejectNWaves.size() == 2) && (tempRejectNWaves[1] == -999)) { |
---|
| 3715 | setWaveNumberListUptoNyquistFreq(whichrow, tempRejectNWaves); |
---|
| 3716 | } |
---|
| 3717 | |
---|
| 3718 | for (uInt i = 0; i < tempAddNWaves.size(); ++i) { |
---|
[2186] | 3719 | bool found = false; |
---|
| 3720 | for (uInt j = 0; j < nWaves.size(); ++j) { |
---|
[2411] | 3721 | if (nWaves[j] == tempAddNWaves[i]) { |
---|
[2186] | 3722 | found = true; |
---|
| 3723 | break; |
---|
| 3724 | } |
---|
| 3725 | } |
---|
[2411] | 3726 | if (!found) nWaves.push_back(tempAddNWaves[i]); |
---|
[2186] | 3727 | } |
---|
| 3728 | |
---|
[2411] | 3729 | for (uInt i = 0; i < tempRejectNWaves.size(); ++i) { |
---|
[2186] | 3730 | for (std::vector<int>::iterator j = nWaves.begin(); j != nWaves.end(); ) { |
---|
[2411] | 3731 | if (*j == tempRejectNWaves[i]) { |
---|
[2186] | 3732 | j = nWaves.erase(j); |
---|
| 3733 | } else { |
---|
| 3734 | ++j; |
---|
| 3735 | } |
---|
| 3736 | } |
---|
| 3737 | } |
---|
| 3738 | |
---|
| 3739 | if (nWaves.size() > 1) { |
---|
| 3740 | sort(nWaves.begin(), nWaves.end()); |
---|
| 3741 | unique(nWaves.begin(), nWaves.end()); |
---|
| 3742 | } |
---|
| 3743 | } |
---|
| 3744 | |
---|
[2411] | 3745 | void Scantable::setWaveNumberListUptoNyquistFreq(const int whichrow, std::vector<int>& nWaves) |
---|
| 3746 | { |
---|
| 3747 | if ((nWaves.size() == 2)&&(nWaves[1] == -999)) { |
---|
| 3748 | int val = nWaves[0]; |
---|
| 3749 | int nyquistFreq = nchan(getIF(whichrow))/2+1; |
---|
| 3750 | nWaves.clear(); |
---|
| 3751 | if (val > nyquistFreq) { // for safety, at least nWaves contains a constant; CAS-3759 |
---|
| 3752 | nWaves.push_back(0); |
---|
| 3753 | } |
---|
| 3754 | while (val <= nyquistFreq) { |
---|
| 3755 | nWaves.push_back(val); |
---|
| 3756 | val++; |
---|
| 3757 | } |
---|
| 3758 | } |
---|
| 3759 | } |
---|
| 3760 | |
---|
[2189] | 3761 | void Scantable::sinusoidBaseline(const std::vector<bool>& mask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, float thresClip, int nIterClip, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2186] | 3762 | { |
---|
[2193] | 3763 | try { |
---|
| 3764 | ofstream ofs; |
---|
| 3765 | String coordInfo = ""; |
---|
| 3766 | bool hasSameNchan = true; |
---|
| 3767 | bool outTextFile = false; |
---|
[2641] | 3768 | bool csvFormat = false; |
---|
[2012] | 3769 | |
---|
[2193] | 3770 | if (blfile != "") { |
---|
[2641] | 3771 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
| 3772 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
[2193] | 3773 | if (ofs) outTextFile = true; |
---|
| 3774 | } |
---|
[2012] | 3775 | |
---|
[2193] | 3776 | if (outLogger || outTextFile) { |
---|
| 3777 | coordInfo = getCoordInfo()[0]; |
---|
| 3778 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 3779 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 3780 | } |
---|
[2012] | 3781 | |
---|
[2193] | 3782 | //Fitter fitter = Fitter(); |
---|
| 3783 | //fitter.setExpression("sinusoid", nWaves); |
---|
| 3784 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2012] | 3785 | |
---|
[2193] | 3786 | int nRow = nrow(); |
---|
| 3787 | std::vector<bool> chanMask; |
---|
| 3788 | std::vector<int> nWaves; |
---|
[2012] | 3789 | |
---|
[2193] | 3790 | bool showProgress; |
---|
| 3791 | int minNRow; |
---|
| 3792 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2189] | 3793 | |
---|
[2193] | 3794 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
| 3795 | chanMask = getCompositeChanMask(whichrow, mask); |
---|
| 3796 | selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves); |
---|
[2186] | 3797 | |
---|
[2193] | 3798 | //FOR DEBUGGING------------ |
---|
[2411] | 3799 | /* |
---|
[2193] | 3800 | if (whichrow < 0) {// == nRow -1) { |
---|
| 3801 | cout << "+++ i=" << setw(3) << whichrow << ", IF=" << setw(2) << getIF(whichrow); |
---|
| 3802 | if (applyFFT) { |
---|
[2186] | 3803 | cout << "[ "; |
---|
| 3804 | for (uInt j = 0; j < nWaves.size(); ++j) { |
---|
| 3805 | cout << nWaves[j] << ", "; |
---|
| 3806 | } |
---|
| 3807 | cout << " ] " << endl; |
---|
[2193] | 3808 | } |
---|
| 3809 | cout << flush; |
---|
[2186] | 3810 | } |
---|
[2411] | 3811 | */ |
---|
[2193] | 3812 | //------------------------- |
---|
| 3813 | |
---|
| 3814 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 3815 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
| 3816 | std::vector<float> params; |
---|
| 3817 | int nClipped = 0; |
---|
| 3818 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual); |
---|
| 3819 | setSpectrum(res, whichrow); |
---|
| 3820 | // |
---|
| 3821 | |
---|
[2641] | 3822 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "sinusoidBaseline()", params, nClipped); |
---|
[2193] | 3823 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[2186] | 3824 | } |
---|
| 3825 | |
---|
[2193] | 3826 | if (outTextFile) ofs.close(); |
---|
[2012] | 3827 | |
---|
[2193] | 3828 | } catch (...) { |
---|
| 3829 | throw; |
---|
[1931] | 3830 | } |
---|
[1907] | 3831 | } |
---|
| 3832 | |
---|
[2189] | 3833 | void Scantable::autoSinusoidBaseline(const std::vector<bool>& mask, const bool applyFFT, const std::string& fftMethod, const std::string& fftThresh, const std::vector<int>& addNWaves, const std::vector<int>& rejectNWaves, float thresClip, int nIterClip, const std::vector<int>& edge, float threshold, int chanAvgLimit, bool getResidual, const std::string& progressInfo, const bool outLogger, const std::string& blfile) |
---|
[2012] | 3834 | { |
---|
[2193] | 3835 | try { |
---|
| 3836 | ofstream ofs; |
---|
| 3837 | String coordInfo = ""; |
---|
| 3838 | bool hasSameNchan = true; |
---|
| 3839 | bool outTextFile = false; |
---|
[2641] | 3840 | bool csvFormat = false; |
---|
[2012] | 3841 | |
---|
[2193] | 3842 | if (blfile != "") { |
---|
[2641] | 3843 | csvFormat = (blfile.substr(0, 1) == "T"); |
---|
| 3844 | ofs.open(blfile.substr(1).c_str(), ios::out | ios::app); |
---|
[2193] | 3845 | if (ofs) outTextFile = true; |
---|
| 3846 | } |
---|
[2012] | 3847 | |
---|
[2193] | 3848 | if (outLogger || outTextFile) { |
---|
| 3849 | coordInfo = getCoordInfo()[0]; |
---|
| 3850 | if (coordInfo == "") coordInfo = "channel"; |
---|
| 3851 | hasSameNchan = hasSameNchanOverIFs(); |
---|
| 3852 | } |
---|
[2012] | 3853 | |
---|
[2193] | 3854 | //Fitter fitter = Fitter(); |
---|
| 3855 | //fitter.setExpression("sinusoid", nWaves); |
---|
| 3856 | //fitter.setIterClipping(thresClip, nIterClip); |
---|
[2012] | 3857 | |
---|
[2193] | 3858 | int nRow = nrow(); |
---|
| 3859 | std::vector<bool> chanMask; |
---|
| 3860 | std::vector<int> nWaves; |
---|
[2186] | 3861 | |
---|
[2193] | 3862 | int minEdgeSize = getIFNos().size()*2; |
---|
| 3863 | STLineFinder lineFinder = STLineFinder(); |
---|
| 3864 | lineFinder.setOptions(threshold, 3, chanAvgLimit); |
---|
[2012] | 3865 | |
---|
[2193] | 3866 | bool showProgress; |
---|
| 3867 | int minNRow; |
---|
| 3868 | parseProgressInfo(progressInfo, showProgress, minNRow); |
---|
[2189] | 3869 | |
---|
[2193] | 3870 | for (int whichrow = 0; whichrow < nRow; ++whichrow) { |
---|
[2012] | 3871 | |
---|
[2193] | 3872 | //------------------------------------------------------- |
---|
| 3873 | //chanMask = getCompositeChanMask(whichrow, mask, edge, minEdgeSize, lineFinder); |
---|
| 3874 | //------------------------------------------------------- |
---|
| 3875 | int edgeSize = edge.size(); |
---|
| 3876 | std::vector<int> currentEdge; |
---|
| 3877 | if (edgeSize >= 2) { |
---|
| 3878 | int idx = 0; |
---|
| 3879 | if (edgeSize > 2) { |
---|
| 3880 | if (edgeSize < minEdgeSize) { |
---|
| 3881 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 3882 | } |
---|
| 3883 | idx = 2 * getIF(whichrow); |
---|
[2012] | 3884 | } |
---|
[2193] | 3885 | currentEdge.push_back(edge[idx]); |
---|
| 3886 | currentEdge.push_back(edge[idx+1]); |
---|
| 3887 | } else { |
---|
| 3888 | throw(AipsError("Wrong length of edge element")); |
---|
[2012] | 3889 | } |
---|
[2193] | 3890 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 3891 | lineFinder.findLines(getCompositeChanMask(whichrow, mask), currentEdge, whichrow); |
---|
| 3892 | chanMask = lineFinder.getMask(); |
---|
| 3893 | //------------------------------------------------------- |
---|
| 3894 | |
---|
| 3895 | selectWaveNumbers(whichrow, chanMask, applyFFT, fftMethod, fftThresh, addNWaves, rejectNWaves, nWaves); |
---|
| 3896 | |
---|
| 3897 | //fitBaseline(chanMask, whichrow, fitter); |
---|
| 3898 | //setSpectrum((getResidual ? fitter.getResidual() : fitter.getFit()), whichrow); |
---|
| 3899 | std::vector<float> params; |
---|
| 3900 | int nClipped = 0; |
---|
| 3901 | std::vector<float> res = doSinusoidFitting(getSpectrum(whichrow), chanMask, nWaves, params, nClipped, thresClip, nIterClip, getResidual); |
---|
| 3902 | setSpectrum(res, whichrow); |
---|
| 3903 | // |
---|
| 3904 | |
---|
[2641] | 3905 | outputFittingResult(outLogger, outTextFile, csvFormat, chanMask, whichrow, coordInfo, hasSameNchan, ofs, "autoSinusoidBaseline()", params, nClipped); |
---|
[2193] | 3906 | showProgressOnTerminal(whichrow, nRow, showProgress, minNRow); |
---|
[2012] | 3907 | } |
---|
| 3908 | |
---|
[2193] | 3909 | if (outTextFile) ofs.close(); |
---|
[2012] | 3910 | |
---|
[2193] | 3911 | } catch (...) { |
---|
| 3912 | throw; |
---|
[2047] | 3913 | } |
---|
| 3914 | } |
---|
| 3915 | |
---|
[2193] | 3916 | std::vector<float> Scantable::doSinusoidFitting(const std::vector<float>& data, const std::vector<bool>& mask, const std::vector<int>& waveNumbers, std::vector<float>& params, int& nClipped, float thresClip, int nIterClip, bool getResidual) |
---|
[2081] | 3917 | { |
---|
[2047] | 3918 | if (data.size() != mask.size()) { |
---|
[2081] | 3919 | throw(AipsError("data and mask sizes are not identical")); |
---|
[2047] | 3920 | } |
---|
[2081] | 3921 | if (data.size() < 2) { |
---|
| 3922 | throw(AipsError("data size is too short")); |
---|
| 3923 | } |
---|
| 3924 | if (waveNumbers.size() == 0) { |
---|
[2186] | 3925 | throw(AipsError("no wave numbers given")); |
---|
[2081] | 3926 | } |
---|
| 3927 | std::vector<int> nWaves; // sorted and uniqued array of wave numbers |
---|
| 3928 | nWaves.reserve(waveNumbers.size()); |
---|
| 3929 | copy(waveNumbers.begin(), waveNumbers.end(), back_inserter(nWaves)); |
---|
| 3930 | sort(nWaves.begin(), nWaves.end()); |
---|
| 3931 | std::vector<int>::iterator end_it = unique(nWaves.begin(), nWaves.end()); |
---|
| 3932 | nWaves.erase(end_it, nWaves.end()); |
---|
| 3933 | |
---|
| 3934 | int minNWaves = nWaves[0]; |
---|
| 3935 | if (minNWaves < 0) { |
---|
[2058] | 3936 | throw(AipsError("wave number must be positive or zero (i.e. constant)")); |
---|
| 3937 | } |
---|
[2081] | 3938 | bool hasConstantTerm = (minNWaves == 0); |
---|
[2047] | 3939 | |
---|
| 3940 | int nChan = data.size(); |
---|
| 3941 | std::vector<int> maskArray; |
---|
| 3942 | std::vector<int> x; |
---|
| 3943 | for (int i = 0; i < nChan; ++i) { |
---|
| 3944 | maskArray.push_back(mask[i] ? 1 : 0); |
---|
| 3945 | if (mask[i]) { |
---|
| 3946 | x.push_back(i); |
---|
| 3947 | } |
---|
| 3948 | } |
---|
| 3949 | |
---|
[2081] | 3950 | int initNData = x.size(); |
---|
[2047] | 3951 | |
---|
[2081] | 3952 | int nData = initNData; |
---|
| 3953 | int nDOF = nWaves.size() * 2 - (hasConstantTerm ? 1 : 0); //number of parameters to solve. |
---|
| 3954 | |
---|
| 3955 | const double PI = 6.0 * asin(0.5); // PI (= 3.141592653...) |
---|
[2186] | 3956 | double baseXFactor = 2.0*PI/(double)(nChan-1); //the denominator (nChan-1) should be changed to (xdata[nChan-1]-xdata[0]) for accepting x-values given in velocity or frequency when this function is moved to fitter. (2011/03/30 WK) |
---|
[2081] | 3957 | |
---|
| 3958 | // xArray : contains elemental values for computing the least-square matrix. |
---|
| 3959 | // xArray.size() is nDOF and xArray[*].size() is nChan. |
---|
| 3960 | // Each xArray element are as follows: |
---|
| 3961 | // xArray[0] = {1.0, 1.0, 1.0, ..., 1.0}, |
---|
| 3962 | // xArray[2n-1] = {sin(nPI/L*x[0]), sin(nPI/L*x[1]), ..., sin(nPI/L*x[nChan])}, |
---|
| 3963 | // xArray[2n] = {cos(nPI/L*x[0]), cos(nPI/L*x[1]), ..., cos(nPI/L*x[nChan])}, |
---|
| 3964 | // where (1 <= n <= nMaxWavesInSW), |
---|
| 3965 | // or, |
---|
| 3966 | // xArray[2n-1] = {sin(wn[n]PI/L*x[0]), sin(wn[n]PI/L*x[1]), ..., sin(wn[n]PI/L*x[nChan])}, |
---|
| 3967 | // xArray[2n] = {cos(wn[n]PI/L*x[0]), cos(wn[n]PI/L*x[1]), ..., cos(wn[n]PI/L*x[nChan])}, |
---|
| 3968 | // where wn[n] denotes waveNumbers[n] (1 <= n <= waveNumbers.size()). |
---|
| 3969 | std::vector<std::vector<double> > xArray; |
---|
| 3970 | if (hasConstantTerm) { |
---|
| 3971 | std::vector<double> xu; |
---|
| 3972 | for (int j = 0; j < nChan; ++j) { |
---|
| 3973 | xu.push_back(1.0); |
---|
| 3974 | } |
---|
| 3975 | xArray.push_back(xu); |
---|
| 3976 | } |
---|
| 3977 | for (uInt i = (hasConstantTerm ? 1 : 0); i < nWaves.size(); ++i) { |
---|
| 3978 | double xFactor = baseXFactor*(double)nWaves[i]; |
---|
| 3979 | std::vector<double> xs, xc; |
---|
| 3980 | xs.clear(); |
---|
| 3981 | xc.clear(); |
---|
| 3982 | for (int j = 0; j < nChan; ++j) { |
---|
| 3983 | xs.push_back(sin(xFactor*(double)j)); |
---|
| 3984 | xc.push_back(cos(xFactor*(double)j)); |
---|
| 3985 | } |
---|
| 3986 | xArray.push_back(xs); |
---|
| 3987 | xArray.push_back(xc); |
---|
| 3988 | } |
---|
| 3989 | |
---|
| 3990 | std::vector<double> z1, r1, residual; |
---|
[2047] | 3991 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 3992 | z1.push_back((double)data[i]); |
---|
[2047] | 3993 | r1.push_back(0.0); |
---|
[2081] | 3994 | residual.push_back(0.0); |
---|
[2047] | 3995 | } |
---|
| 3996 | |
---|
| 3997 | for (int nClip = 0; nClip < nIterClip+1; ++nClip) { |
---|
[2081] | 3998 | // xMatrix : horizontal concatenation of |
---|
| 3999 | // the least-sq. matrix (left) and an |
---|
| 4000 | // identity matrix (right). |
---|
| 4001 | // the right part is used to calculate the inverse matrix of the left part. |
---|
[2047] | 4002 | double xMatrix[nDOF][2*nDOF]; |
---|
| 4003 | double zMatrix[nDOF]; |
---|
| 4004 | for (int i = 0; i < nDOF; ++i) { |
---|
| 4005 | for (int j = 0; j < 2*nDOF; ++j) { |
---|
| 4006 | xMatrix[i][j] = 0.0; |
---|
[2012] | 4007 | } |
---|
[2047] | 4008 | xMatrix[i][nDOF+i] = 1.0; |
---|
| 4009 | zMatrix[i] = 0.0; |
---|
| 4010 | } |
---|
| 4011 | |
---|
[2193] | 4012 | int nUseData = 0; |
---|
[2081] | 4013 | for (int k = 0; k < nChan; ++k) { |
---|
| 4014 | if (maskArray[k] == 0) continue; |
---|
| 4015 | |
---|
| 4016 | for (int i = 0; i < nDOF; ++i) { |
---|
| 4017 | for (int j = i; j < nDOF; ++j) { |
---|
| 4018 | xMatrix[i][j] += xArray[i][k] * xArray[j][k]; |
---|
| 4019 | } |
---|
| 4020 | zMatrix[i] += z1[k] * xArray[i][k]; |
---|
| 4021 | } |
---|
[2193] | 4022 | |
---|
| 4023 | nUseData++; |
---|
[2047] | 4024 | } |
---|
| 4025 | |
---|
[2193] | 4026 | if (nUseData < 1) { |
---|
| 4027 | throw(AipsError("all channels clipped or masked. can't execute fitting anymore.")); |
---|
| 4028 | } |
---|
| 4029 | |
---|
[2047] | 4030 | for (int i = 0; i < nDOF; ++i) { |
---|
| 4031 | for (int j = 0; j < i; ++j) { |
---|
| 4032 | xMatrix[i][j] = xMatrix[j][i]; |
---|
[2012] | 4033 | } |
---|
| 4034 | } |
---|
| 4035 | |
---|
[2047] | 4036 | std::vector<double> invDiag; |
---|
| 4037 | for (int i = 0; i < nDOF; ++i) { |
---|
| 4038 | invDiag.push_back(1.0/xMatrix[i][i]); |
---|
| 4039 | for (int j = 0; j < nDOF; ++j) { |
---|
| 4040 | xMatrix[i][j] *= invDiag[i]; |
---|
| 4041 | } |
---|
| 4042 | } |
---|
| 4043 | |
---|
| 4044 | for (int k = 0; k < nDOF; ++k) { |
---|
| 4045 | for (int i = 0; i < nDOF; ++i) { |
---|
| 4046 | if (i != k) { |
---|
| 4047 | double factor1 = xMatrix[k][k]; |
---|
| 4048 | double factor2 = xMatrix[i][k]; |
---|
| 4049 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 4050 | xMatrix[i][j] *= factor1; |
---|
| 4051 | xMatrix[i][j] -= xMatrix[k][j]*factor2; |
---|
| 4052 | xMatrix[i][j] /= factor1; |
---|
| 4053 | } |
---|
| 4054 | } |
---|
| 4055 | } |
---|
| 4056 | double xDiag = xMatrix[k][k]; |
---|
| 4057 | for (int j = k; j < 2*nDOF; ++j) { |
---|
| 4058 | xMatrix[k][j] /= xDiag; |
---|
| 4059 | } |
---|
| 4060 | } |
---|
| 4061 | |
---|
| 4062 | for (int i = 0; i < nDOF; ++i) { |
---|
| 4063 | for (int j = 0; j < nDOF; ++j) { |
---|
| 4064 | xMatrix[i][nDOF+j] *= invDiag[j]; |
---|
| 4065 | } |
---|
| 4066 | } |
---|
| 4067 | //compute a vector y which consists of the coefficients of the sinusoids forming the |
---|
[2081] | 4068 | //best-fit curves (a0,s1,c1,s2,c2,...), where a0 is constant and s* and c* are of sine |
---|
| 4069 | //and cosine functions, respectively. |
---|
[2047] | 4070 | std::vector<double> y; |
---|
[2081] | 4071 | params.clear(); |
---|
[2047] | 4072 | for (int i = 0; i < nDOF; ++i) { |
---|
| 4073 | y.push_back(0.0); |
---|
| 4074 | for (int j = 0; j < nDOF; ++j) { |
---|
| 4075 | y[i] += xMatrix[i][nDOF+j]*zMatrix[j]; |
---|
| 4076 | } |
---|
[2081] | 4077 | params.push_back(y[i]); |
---|
[2047] | 4078 | } |
---|
| 4079 | |
---|
| 4080 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 4081 | r1[i] = y[0]; |
---|
| 4082 | for (int j = 1; j < nDOF; ++j) { |
---|
| 4083 | r1[i] += y[j]*xArray[j][i]; |
---|
| 4084 | } |
---|
| 4085 | residual[i] = z1[i] - r1[i]; |
---|
[2047] | 4086 | } |
---|
| 4087 | |
---|
| 4088 | if ((nClip == nIterClip) || (thresClip <= 0.0)) { |
---|
| 4089 | break; |
---|
| 4090 | } else { |
---|
| 4091 | double stdDev = 0.0; |
---|
| 4092 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 4093 | stdDev += residual[i]*residual[i]*(double)maskArray[i]; |
---|
[2047] | 4094 | } |
---|
| 4095 | stdDev = sqrt(stdDev/(double)nData); |
---|
| 4096 | |
---|
| 4097 | double thres = stdDev * thresClip; |
---|
| 4098 | int newNData = 0; |
---|
| 4099 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 4100 | if (abs(residual[i]) >= thres) { |
---|
[2047] | 4101 | maskArray[i] = 0; |
---|
| 4102 | } |
---|
| 4103 | if (maskArray[i] > 0) { |
---|
| 4104 | newNData++; |
---|
| 4105 | } |
---|
| 4106 | } |
---|
[2081] | 4107 | if (newNData == nData) { |
---|
| 4108 | break; //no more flag to add. iteration stops. |
---|
[2047] | 4109 | } else { |
---|
[2081] | 4110 | nData = newNData; |
---|
[2047] | 4111 | } |
---|
| 4112 | } |
---|
[2012] | 4113 | } |
---|
| 4114 | |
---|
[2193] | 4115 | nClipped = initNData - nData; |
---|
| 4116 | |
---|
[2058] | 4117 | std::vector<float> result; |
---|
| 4118 | if (getResidual) { |
---|
| 4119 | for (int i = 0; i < nChan; ++i) { |
---|
[2081] | 4120 | result.push_back((float)residual[i]); |
---|
[2058] | 4121 | } |
---|
| 4122 | } else { |
---|
| 4123 | for (int i = 0; i < nChan; ++i) { |
---|
| 4124 | result.push_back((float)r1[i]); |
---|
| 4125 | } |
---|
[2047] | 4126 | } |
---|
| 4127 | |
---|
[2058] | 4128 | return result; |
---|
[2012] | 4129 | } |
---|
| 4130 | |
---|
[2047] | 4131 | void Scantable::fitBaseline(const std::vector<bool>& mask, int whichrow, Fitter& fitter) |
---|
| 4132 | { |
---|
[2081] | 4133 | std::vector<double> dAbcissa = getAbcissa(whichrow); |
---|
| 4134 | std::vector<float> abcissa; |
---|
| 4135 | for (uInt i = 0; i < dAbcissa.size(); ++i) { |
---|
| 4136 | abcissa.push_back((float)dAbcissa[i]); |
---|
[2047] | 4137 | } |
---|
| 4138 | std::vector<float> spec = getSpectrum(whichrow); |
---|
[2012] | 4139 | |
---|
[2081] | 4140 | fitter.setData(abcissa, spec, mask); |
---|
[2047] | 4141 | fitter.lfit(); |
---|
| 4142 | } |
---|
| 4143 | |
---|
| 4144 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask) |
---|
| 4145 | { |
---|
[2591] | 4146 | /**** |
---|
| 4147 | double ms1TimeStart, ms1TimeEnd, ms2TimeStart, ms2TimeEnd; |
---|
| 4148 | double elapse1 = 0.0; |
---|
| 4149 | double elapse2 = 0.0; |
---|
| 4150 | |
---|
| 4151 | ms1TimeStart = mathutil::gettimeofday_sec(); |
---|
| 4152 | ****/ |
---|
| 4153 | |
---|
[2186] | 4154 | std::vector<bool> mask = getMask(whichrow); |
---|
[2591] | 4155 | |
---|
| 4156 | /**** |
---|
| 4157 | ms1TimeEnd = mathutil::gettimeofday_sec(); |
---|
| 4158 | elapse1 = ms1TimeEnd - ms1TimeStart; |
---|
| 4159 | std::cout << "ms1 : " << elapse1 << " (sec.)" << endl; |
---|
| 4160 | ms2TimeStart = mathutil::gettimeofday_sec(); |
---|
| 4161 | ****/ |
---|
| 4162 | |
---|
[2186] | 4163 | uInt maskSize = mask.size(); |
---|
[2410] | 4164 | if (inMask.size() != 0) { |
---|
| 4165 | if (maskSize != inMask.size()) { |
---|
| 4166 | throw(AipsError("mask sizes are not the same.")); |
---|
| 4167 | } |
---|
| 4168 | for (uInt i = 0; i < maskSize; ++i) { |
---|
| 4169 | mask[i] = mask[i] && inMask[i]; |
---|
| 4170 | } |
---|
[2047] | 4171 | } |
---|
| 4172 | |
---|
[2591] | 4173 | /**** |
---|
| 4174 | ms2TimeEnd = mathutil::gettimeofday_sec(); |
---|
| 4175 | elapse2 = ms2TimeEnd - ms2TimeStart; |
---|
| 4176 | std::cout << "ms2 : " << elapse2 << " (sec.)" << endl; |
---|
| 4177 | ****/ |
---|
| 4178 | |
---|
[2186] | 4179 | return mask; |
---|
[2047] | 4180 | } |
---|
| 4181 | |
---|
| 4182 | /* |
---|
| 4183 | std::vector<bool> Scantable::getCompositeChanMask(int whichrow, const std::vector<bool>& inMask, const std::vector<int>& edge, const int minEdgeSize, STLineFinder& lineFinder) |
---|
| 4184 | { |
---|
| 4185 | int edgeSize = edge.size(); |
---|
| 4186 | std::vector<int> currentEdge; |
---|
| 4187 | if (edgeSize >= 2) { |
---|
| 4188 | int idx = 0; |
---|
| 4189 | if (edgeSize > 2) { |
---|
| 4190 | if (edgeSize < minEdgeSize) { |
---|
| 4191 | throw(AipsError("Length of edge element info is less than that of IFs")); |
---|
| 4192 | } |
---|
| 4193 | idx = 2 * getIF(whichrow); |
---|
| 4194 | } |
---|
| 4195 | currentEdge.push_back(edge[idx]); |
---|
| 4196 | currentEdge.push_back(edge[idx+1]); |
---|
| 4197 | } else { |
---|
| 4198 | throw(AipsError("Wrong length of edge element")); |
---|
| 4199 | } |
---|
| 4200 | |
---|
| 4201 | lineFinder.setData(getSpectrum(whichrow)); |
---|
| 4202 | lineFinder.findLines(getCompositeChanMask(whichrow, inMask), currentEdge, whichrow); |
---|
| 4203 | |
---|
| 4204 | return lineFinder.getMask(); |
---|
| 4205 | } |
---|
| 4206 | */ |
---|
| 4207 | |
---|
| 4208 | /* for poly. the variations of outputFittingResult() should be merged into one eventually (2011/3/10 WK) */ |
---|
[2641] | 4209 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, Fitter& fitter) |
---|
[2186] | 4210 | { |
---|
[2047] | 4211 | if (outLogger || outTextFile) { |
---|
| 4212 | std::vector<float> params = fitter.getParameters(); |
---|
| 4213 | std::vector<bool> fixed = fitter.getFixedParameters(); |
---|
| 4214 | float rms = getRms(chanMask, whichrow); |
---|
| 4215 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
| 4216 | |
---|
| 4217 | if (outLogger) { |
---|
| 4218 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
[2641] | 4219 | ols << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, false, csvFormat) << LogIO::POST ; |
---|
[2047] | 4220 | } |
---|
| 4221 | if (outTextFile) { |
---|
[2641] | 4222 | ofs << formatBaselineParams(params, fixed, rms, -1, masklist, whichrow, true, csvFormat) << flush; |
---|
[2047] | 4223 | } |
---|
| 4224 | } |
---|
| 4225 | } |
---|
| 4226 | |
---|
| 4227 | /* for cspline. will be merged once cspline is available in fitter (2011/3/10 WK) */ |
---|
[2641] | 4228 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, const std::vector<int>& edge, const std::vector<float>& params, const int nClipped) |
---|
[2186] | 4229 | { |
---|
[2047] | 4230 | if (outLogger || outTextFile) { |
---|
[2591] | 4231 | /**** |
---|
| 4232 | double ms1TimeStart, ms1TimeEnd, ms2TimeStart, ms2TimeEnd; |
---|
| 4233 | double elapse1 = 0.0; |
---|
| 4234 | double elapse2 = 0.0; |
---|
| 4235 | |
---|
| 4236 | ms1TimeStart = mathutil::gettimeofday_sec(); |
---|
| 4237 | ****/ |
---|
| 4238 | |
---|
[2047] | 4239 | float rms = getRms(chanMask, whichrow); |
---|
[2591] | 4240 | |
---|
| 4241 | /**** |
---|
| 4242 | ms1TimeEnd = mathutil::gettimeofday_sec(); |
---|
| 4243 | elapse1 = ms1TimeEnd - ms1TimeStart; |
---|
| 4244 | std::cout << "ot1 : " << elapse1 << " (sec.)" << endl; |
---|
| 4245 | ms2TimeStart = mathutil::gettimeofday_sec(); |
---|
| 4246 | ****/ |
---|
| 4247 | |
---|
[2047] | 4248 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
[2081] | 4249 | std::vector<bool> fixed; |
---|
| 4250 | fixed.clear(); |
---|
[2047] | 4251 | |
---|
| 4252 | if (outLogger) { |
---|
| 4253 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
[2641] | 4254 | ols << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, false, csvFormat) << LogIO::POST ; |
---|
[2047] | 4255 | } |
---|
| 4256 | if (outTextFile) { |
---|
[2641] | 4257 | ofs << formatPiecewiseBaselineParams(edge, params, fixed, rms, nClipped, masklist, whichrow, true, csvFormat) << flush; |
---|
[2047] | 4258 | } |
---|
[2591] | 4259 | |
---|
| 4260 | /**** |
---|
| 4261 | ms2TimeEnd = mathutil::gettimeofday_sec(); |
---|
| 4262 | elapse2 = ms2TimeEnd - ms2TimeStart; |
---|
| 4263 | std::cout << "ot2 : " << elapse2 << " (sec.)" << endl; |
---|
| 4264 | ****/ |
---|
| 4265 | |
---|
[2047] | 4266 | } |
---|
| 4267 | } |
---|
| 4268 | |
---|
[2645] | 4269 | /* for chebyshev/sinusoid. will be merged once chebyshev/sinusoid is available in fitter (2011/3/10 WK) */ |
---|
[2641] | 4270 | void Scantable::outputFittingResult(bool outLogger, bool outTextFile, bool csvFormat, const std::vector<bool>& chanMask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, ofstream& ofs, const casa::String& funcName, const std::vector<float>& params, const int nClipped) |
---|
[2186] | 4271 | { |
---|
[2047] | 4272 | if (outLogger || outTextFile) { |
---|
| 4273 | float rms = getRms(chanMask, whichrow); |
---|
| 4274 | String masklist = getMaskRangeList(chanMask, whichrow, coordInfo, hasSameNchan); |
---|
[2081] | 4275 | std::vector<bool> fixed; |
---|
| 4276 | fixed.clear(); |
---|
[2047] | 4277 | |
---|
| 4278 | if (outLogger) { |
---|
| 4279 | LogIO ols(LogOrigin("Scantable", funcName, WHERE)); |
---|
[2641] | 4280 | ols << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, false, csvFormat) << LogIO::POST ; |
---|
[2047] | 4281 | } |
---|
| 4282 | if (outTextFile) { |
---|
[2641] | 4283 | ofs << formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, true, csvFormat) << flush; |
---|
[2047] | 4284 | } |
---|
| 4285 | } |
---|
| 4286 | } |
---|
| 4287 | |
---|
[2189] | 4288 | void Scantable::parseProgressInfo(const std::string& progressInfo, bool& showProgress, int& minNRow) |
---|
[2186] | 4289 | { |
---|
[2189] | 4290 | int idxDelimiter = progressInfo.find(","); |
---|
| 4291 | if (idxDelimiter < 0) { |
---|
| 4292 | throw(AipsError("wrong value in 'showprogress' parameter")) ; |
---|
| 4293 | } |
---|
| 4294 | showProgress = (progressInfo.substr(0, idxDelimiter) == "true"); |
---|
| 4295 | std::istringstream is(progressInfo.substr(idxDelimiter+1)); |
---|
| 4296 | is >> minNRow; |
---|
| 4297 | } |
---|
| 4298 | |
---|
| 4299 | void Scantable::showProgressOnTerminal(const int nProcessed, const int nTotal, const bool showProgress, const int nTotalThreshold) |
---|
| 4300 | { |
---|
| 4301 | if (showProgress && (nTotal >= nTotalThreshold)) { |
---|
[2186] | 4302 | int nInterval = int(floor(double(nTotal)/100.0)); |
---|
| 4303 | if (nInterval == 0) nInterval++; |
---|
| 4304 | |
---|
[2193] | 4305 | if (nProcessed % nInterval == 0) { |
---|
[2189] | 4306 | printf("\r"); //go to the head of line |
---|
[2186] | 4307 | printf("\x1b[31m\x1b[1m"); //set red color, highlighted |
---|
[2189] | 4308 | printf("[%3d%%]", (int)(100.0*(double(nProcessed+1))/(double(nTotal))) ); |
---|
| 4309 | printf("\x1b[39m\x1b[0m"); //set default attributes |
---|
[2186] | 4310 | fflush(NULL); |
---|
| 4311 | } |
---|
[2193] | 4312 | |
---|
[2186] | 4313 | if (nProcessed == nTotal - 1) { |
---|
| 4314 | printf("\r\x1b[K"); //clear |
---|
| 4315 | fflush(NULL); |
---|
| 4316 | } |
---|
[2193] | 4317 | |
---|
[2186] | 4318 | } |
---|
| 4319 | } |
---|
| 4320 | |
---|
| 4321 | std::vector<float> Scantable::execFFT(const int whichrow, const std::vector<bool>& inMask, bool getRealImag, bool getAmplitudeOnly) |
---|
| 4322 | { |
---|
| 4323 | std::vector<bool> mask = getMask(whichrow); |
---|
| 4324 | |
---|
| 4325 | if (inMask.size() > 0) { |
---|
| 4326 | uInt maskSize = mask.size(); |
---|
| 4327 | if (maskSize != inMask.size()) { |
---|
| 4328 | throw(AipsError("mask sizes are not the same.")); |
---|
| 4329 | } |
---|
| 4330 | for (uInt i = 0; i < maskSize; ++i) { |
---|
| 4331 | mask[i] = mask[i] && inMask[i]; |
---|
| 4332 | } |
---|
| 4333 | } |
---|
| 4334 | |
---|
| 4335 | Vector<Float> spec = getSpectrum(whichrow); |
---|
| 4336 | mathutil::doZeroOrderInterpolation(spec, mask); |
---|
| 4337 | |
---|
| 4338 | FFTServer<Float,Complex> ffts; |
---|
| 4339 | Vector<Complex> fftres; |
---|
| 4340 | ffts.fft0(fftres, spec); |
---|
| 4341 | |
---|
| 4342 | std::vector<float> res; |
---|
| 4343 | float norm = float(2.0/double(spec.size())); |
---|
| 4344 | |
---|
| 4345 | if (getRealImag) { |
---|
| 4346 | for (uInt i = 0; i < fftres.size(); ++i) { |
---|
| 4347 | res.push_back(real(fftres[i])*norm); |
---|
| 4348 | res.push_back(imag(fftres[i])*norm); |
---|
| 4349 | } |
---|
| 4350 | } else { |
---|
| 4351 | for (uInt i = 0; i < fftres.size(); ++i) { |
---|
| 4352 | res.push_back(abs(fftres[i])*norm); |
---|
| 4353 | if (!getAmplitudeOnly) res.push_back(arg(fftres[i])); |
---|
| 4354 | } |
---|
| 4355 | } |
---|
| 4356 | |
---|
| 4357 | return res; |
---|
| 4358 | } |
---|
| 4359 | |
---|
| 4360 | |
---|
| 4361 | float Scantable::getRms(const std::vector<bool>& mask, int whichrow) |
---|
| 4362 | { |
---|
[2591] | 4363 | /**** |
---|
[2737] | 4364 | double ms1TimeStart, ms1TimeEnd; |
---|
[2591] | 4365 | double elapse1 = 0.0; |
---|
| 4366 | ms1TimeStart = mathutil::gettimeofday_sec(); |
---|
| 4367 | ****/ |
---|
| 4368 | |
---|
[2012] | 4369 | Vector<Float> spec; |
---|
| 4370 | specCol_.get(whichrow, spec); |
---|
| 4371 | |
---|
[2591] | 4372 | /**** |
---|
| 4373 | ms1TimeEnd = mathutil::gettimeofday_sec(); |
---|
| 4374 | elapse1 = ms1TimeEnd - ms1TimeStart; |
---|
| 4375 | std::cout << "rm1 : " << elapse1 << " (sec.)" << endl; |
---|
| 4376 | ****/ |
---|
| 4377 | |
---|
[2737] | 4378 | return (float)doGetRms(mask, spec); |
---|
| 4379 | } |
---|
| 4380 | |
---|
| 4381 | double Scantable::doGetRms(const std::vector<bool>& mask, const Vector<Float>& spec) |
---|
| 4382 | { |
---|
| 4383 | double mean = 0.0; |
---|
| 4384 | double smean = 0.0; |
---|
[2012] | 4385 | int n = 0; |
---|
[2047] | 4386 | for (uInt i = 0; i < spec.nelements(); ++i) { |
---|
[2012] | 4387 | if (mask[i]) { |
---|
[2737] | 4388 | double val = (double)spec[i]; |
---|
| 4389 | mean += val; |
---|
| 4390 | smean += val*val; |
---|
[2012] | 4391 | n++; |
---|
| 4392 | } |
---|
| 4393 | } |
---|
| 4394 | |
---|
[2737] | 4395 | mean /= (double)n; |
---|
| 4396 | smean /= (double)n; |
---|
[2012] | 4397 | |
---|
| 4398 | return sqrt(smean - mean*mean); |
---|
| 4399 | } |
---|
| 4400 | |
---|
[2641] | 4401 | std::string Scantable::formatBaselineParamsHeader(int whichrow, const std::string& masklist, bool verbose, bool csvformat) const |
---|
[2012] | 4402 | { |
---|
[2641] | 4403 | if (verbose) { |
---|
| 4404 | ostringstream oss; |
---|
[2012] | 4405 | |
---|
[2641] | 4406 | if (csvformat) { |
---|
| 4407 | oss << getScan(whichrow) << ","; |
---|
| 4408 | oss << getBeam(whichrow) << ","; |
---|
| 4409 | oss << getIF(whichrow) << ","; |
---|
| 4410 | oss << getPol(whichrow) << ","; |
---|
| 4411 | oss << getCycle(whichrow) << ","; |
---|
| 4412 | String commaReplacedMasklist = masklist; |
---|
| 4413 | string::size_type pos = 0; |
---|
| 4414 | while (pos = commaReplacedMasklist.find(","), pos != string::npos) { |
---|
| 4415 | commaReplacedMasklist.replace(pos, 1, ";"); |
---|
| 4416 | pos++; |
---|
| 4417 | } |
---|
| 4418 | oss << commaReplacedMasklist << ","; |
---|
| 4419 | } else { |
---|
| 4420 | oss << " Scan[" << getScan(whichrow) << "]"; |
---|
| 4421 | oss << " Beam[" << getBeam(whichrow) << "]"; |
---|
| 4422 | oss << " IF[" << getIF(whichrow) << "]"; |
---|
| 4423 | oss << " Pol[" << getPol(whichrow) << "]"; |
---|
| 4424 | oss << " Cycle[" << getCycle(whichrow) << "]: " << endl; |
---|
| 4425 | oss << "Fitter range = " << masklist << endl; |
---|
| 4426 | oss << "Baseline parameters" << endl; |
---|
| 4427 | } |
---|
[2012] | 4428 | oss << flush; |
---|
[2641] | 4429 | |
---|
| 4430 | return String(oss); |
---|
[2012] | 4431 | } |
---|
| 4432 | |
---|
[2641] | 4433 | return ""; |
---|
[2012] | 4434 | } |
---|
| 4435 | |
---|
[2641] | 4436 | std::string Scantable::formatBaselineParamsFooter(float rms, int nClipped, bool verbose, bool csvformat) const |
---|
[2012] | 4437 | { |
---|
[2641] | 4438 | if (verbose) { |
---|
| 4439 | ostringstream oss; |
---|
[2012] | 4440 | |
---|
[2641] | 4441 | if (csvformat) { |
---|
| 4442 | oss << rms << ","; |
---|
| 4443 | if (nClipped >= 0) { |
---|
| 4444 | oss << nClipped; |
---|
| 4445 | } |
---|
| 4446 | } else { |
---|
| 4447 | oss << "Results of baseline fit" << endl; |
---|
| 4448 | oss << " rms = " << setprecision(6) << rms << endl; |
---|
| 4449 | if (nClipped >= 0) { |
---|
| 4450 | oss << " Number of clipped channels = " << nClipped << endl; |
---|
| 4451 | } |
---|
| 4452 | for (int i = 0; i < 60; ++i) { |
---|
| 4453 | oss << "-"; |
---|
| 4454 | } |
---|
[2193] | 4455 | } |
---|
[2131] | 4456 | oss << endl; |
---|
[2094] | 4457 | oss << flush; |
---|
[2641] | 4458 | |
---|
| 4459 | return String(oss); |
---|
[2012] | 4460 | } |
---|
| 4461 | |
---|
[2641] | 4462 | return ""; |
---|
[2012] | 4463 | } |
---|
| 4464 | |
---|
[2186] | 4465 | std::string Scantable::formatBaselineParams(const std::vector<float>& params, |
---|
| 4466 | const std::vector<bool>& fixed, |
---|
| 4467 | float rms, |
---|
[2193] | 4468 | int nClipped, |
---|
[2186] | 4469 | const std::string& masklist, |
---|
| 4470 | int whichrow, |
---|
| 4471 | bool verbose, |
---|
[2641] | 4472 | bool csvformat, |
---|
[2186] | 4473 | int start, int count, |
---|
| 4474 | bool resetparamid) const |
---|
[2047] | 4475 | { |
---|
[2064] | 4476 | int nParam = (int)(params.size()); |
---|
[2047] | 4477 | |
---|
[2064] | 4478 | if (nParam < 1) { |
---|
| 4479 | return(" Not fitted"); |
---|
| 4480 | } else { |
---|
| 4481 | |
---|
| 4482 | ostringstream oss; |
---|
[2641] | 4483 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat); |
---|
[2064] | 4484 | |
---|
| 4485 | if (start < 0) start = 0; |
---|
| 4486 | if (count < 0) count = nParam; |
---|
| 4487 | int end = start + count; |
---|
| 4488 | if (end > nParam) end = nParam; |
---|
| 4489 | int paramidoffset = (resetparamid) ? (-start) : 0; |
---|
| 4490 | |
---|
| 4491 | for (int i = start; i < end; ++i) { |
---|
| 4492 | if (i > start) { |
---|
[2047] | 4493 | oss << ","; |
---|
| 4494 | } |
---|
[2064] | 4495 | std::string sFix = ((fixed.size() > 0) && (fixed[i]) && verbose) ? "(fixed)" : ""; |
---|
[2641] | 4496 | if (csvformat) { |
---|
| 4497 | oss << params[i] << sFix; |
---|
| 4498 | } else { |
---|
| 4499 | oss << " p" << (i+paramidoffset) << sFix << "= " << right << setw(13) << setprecision(6) << params[i]; |
---|
| 4500 | } |
---|
[2047] | 4501 | } |
---|
[2064] | 4502 | |
---|
[2641] | 4503 | if (csvformat) { |
---|
| 4504 | oss << ","; |
---|
[2644] | 4505 | } else { |
---|
| 4506 | oss << endl; |
---|
[2641] | 4507 | } |
---|
| 4508 | oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat); |
---|
[2064] | 4509 | |
---|
| 4510 | return String(oss); |
---|
[2047] | 4511 | } |
---|
| 4512 | |
---|
| 4513 | } |
---|
| 4514 | |
---|
[2641] | 4515 | std::string Scantable::formatPiecewiseBaselineParams(const std::vector<int>& ranges, const std::vector<float>& params, const std::vector<bool>& fixed, float rms, int nClipped, const std::string& masklist, int whichrow, bool verbose, bool csvformat) const |
---|
[2012] | 4516 | { |
---|
[2064] | 4517 | int nOutParam = (int)(params.size()); |
---|
| 4518 | int nPiece = (int)(ranges.size()) - 1; |
---|
[2012] | 4519 | |
---|
[2064] | 4520 | if (nOutParam < 1) { |
---|
| 4521 | return(" Not fitted"); |
---|
| 4522 | } else if (nPiece < 0) { |
---|
[2641] | 4523 | return formatBaselineParams(params, fixed, rms, nClipped, masklist, whichrow, verbose, csvformat); |
---|
[2064] | 4524 | } else if (nPiece < 1) { |
---|
| 4525 | return(" Bad count of the piece edge info"); |
---|
| 4526 | } else if (nOutParam % nPiece != 0) { |
---|
| 4527 | return(" Bad count of the output baseline parameters"); |
---|
| 4528 | } else { |
---|
| 4529 | |
---|
| 4530 | int nParam = nOutParam / nPiece; |
---|
| 4531 | |
---|
| 4532 | ostringstream oss; |
---|
[2641] | 4533 | oss << formatBaselineParamsHeader(whichrow, masklist, verbose, csvformat); |
---|
[2064] | 4534 | |
---|
[2641] | 4535 | if (csvformat) { |
---|
| 4536 | for (int i = 0; i < nPiece; ++i) { |
---|
| 4537 | oss << ranges[i] << "," << (ranges[i+1]-1) << ","; |
---|
| 4538 | oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true); |
---|
| 4539 | } |
---|
| 4540 | } else { |
---|
| 4541 | stringstream ss; |
---|
| 4542 | ss << ranges[nPiece] << flush; |
---|
| 4543 | int wRange = ss.str().size() * 2 + 5; |
---|
[2064] | 4544 | |
---|
[2641] | 4545 | for (int i = 0; i < nPiece; ++i) { |
---|
| 4546 | ss.str(""); |
---|
| 4547 | ss << " [" << ranges[i] << "," << (ranges[i+1]-1) << "]"; |
---|
| 4548 | oss << left << setw(wRange) << ss.str(); |
---|
| 4549 | oss << formatBaselineParams(params, fixed, rms, 0, masklist, whichrow, false, csvformat, i*nParam, nParam, true); |
---|
[2644] | 4550 | //oss << endl; |
---|
[2641] | 4551 | } |
---|
[2012] | 4552 | } |
---|
[2064] | 4553 | |
---|
[2641] | 4554 | oss << formatBaselineParamsFooter(rms, nClipped, verbose, csvformat); |
---|
[2064] | 4555 | |
---|
| 4556 | return String(oss); |
---|
[2012] | 4557 | } |
---|
| 4558 | |
---|
| 4559 | } |
---|
| 4560 | |
---|
[2047] | 4561 | bool Scantable::hasSameNchanOverIFs() |
---|
[2012] | 4562 | { |
---|
[2047] | 4563 | int nIF = nif(-1); |
---|
| 4564 | int nCh; |
---|
| 4565 | int totalPositiveNChan = 0; |
---|
| 4566 | int nPositiveNChan = 0; |
---|
[2012] | 4567 | |
---|
[2047] | 4568 | for (int i = 0; i < nIF; ++i) { |
---|
| 4569 | nCh = nchan(i); |
---|
| 4570 | if (nCh > 0) { |
---|
| 4571 | totalPositiveNChan += nCh; |
---|
| 4572 | nPositiveNChan++; |
---|
[2012] | 4573 | } |
---|
| 4574 | } |
---|
| 4575 | |
---|
[2047] | 4576 | return (totalPositiveNChan == (nPositiveNChan * nchan(0))); |
---|
[2012] | 4577 | } |
---|
| 4578 | |
---|
[2047] | 4579 | std::string Scantable::getMaskRangeList(const std::vector<bool>& mask, int whichrow, const casa::String& coordInfo, bool hasSameNchan, bool verbose) |
---|
[2012] | 4580 | { |
---|
[2427] | 4581 | if (mask.size() <= 0) { |
---|
| 4582 | throw(AipsError("The mask elements should be > 0")); |
---|
[2012] | 4583 | } |
---|
[2047] | 4584 | int IF = getIF(whichrow); |
---|
| 4585 | if (mask.size() != (uInt)nchan(IF)) { |
---|
[2012] | 4586 | throw(AipsError("Number of channels in scantable != number of mask elements")); |
---|
| 4587 | } |
---|
| 4588 | |
---|
[2047] | 4589 | if (verbose) { |
---|
[2012] | 4590 | LogIO logOs(LogOrigin("Scantable", "getMaskRangeList()", WHERE)); |
---|
| 4591 | logOs << LogIO::WARN << "The current mask window unit is " << coordInfo; |
---|
| 4592 | if (!hasSameNchan) { |
---|
[2047] | 4593 | logOs << endl << "This mask is only valid for IF=" << IF; |
---|
[2012] | 4594 | } |
---|
| 4595 | logOs << LogIO::POST; |
---|
| 4596 | } |
---|
| 4597 | |
---|
| 4598 | std::vector<double> abcissa = getAbcissa(whichrow); |
---|
[2047] | 4599 | std::vector<int> edge = getMaskEdgeIndices(mask); |
---|
| 4600 | |
---|
[2012] | 4601 | ostringstream oss; |
---|
| 4602 | oss.setf(ios::fixed); |
---|
| 4603 | oss << setprecision(1) << "["; |
---|
[2047] | 4604 | for (uInt i = 0; i < edge.size(); i+=2) { |
---|
[2012] | 4605 | if (i > 0) oss << ","; |
---|
[2047] | 4606 | oss << "[" << (float)abcissa[edge[i]] << "," << (float)abcissa[edge[i+1]] << "]"; |
---|
[2012] | 4607 | } |
---|
| 4608 | oss << "]" << flush; |
---|
| 4609 | |
---|
| 4610 | return String(oss); |
---|
| 4611 | } |
---|
| 4612 | |
---|
[2047] | 4613 | std::vector<int> Scantable::getMaskEdgeIndices(const std::vector<bool>& mask) |
---|
[2012] | 4614 | { |
---|
[2427] | 4615 | if (mask.size() <= 0) { |
---|
| 4616 | throw(AipsError("The mask elements should be > 0")); |
---|
[2012] | 4617 | } |
---|
| 4618 | |
---|
[2047] | 4619 | std::vector<int> out, startIndices, endIndices; |
---|
| 4620 | int maskSize = mask.size(); |
---|
[2012] | 4621 | |
---|
[2047] | 4622 | startIndices.clear(); |
---|
| 4623 | endIndices.clear(); |
---|
| 4624 | |
---|
| 4625 | if (mask[0]) { |
---|
| 4626 | startIndices.push_back(0); |
---|
[2012] | 4627 | } |
---|
[2047] | 4628 | for (int i = 1; i < maskSize; ++i) { |
---|
| 4629 | if ((!mask[i-1]) && mask[i]) { |
---|
| 4630 | startIndices.push_back(i); |
---|
| 4631 | } else if (mask[i-1] && (!mask[i])) { |
---|
| 4632 | endIndices.push_back(i-1); |
---|
| 4633 | } |
---|
[2012] | 4634 | } |
---|
[2047] | 4635 | if (mask[maskSize-1]) { |
---|
| 4636 | endIndices.push_back(maskSize-1); |
---|
| 4637 | } |
---|
[2012] | 4638 | |
---|
[2047] | 4639 | if (startIndices.size() != endIndices.size()) { |
---|
| 4640 | throw(AipsError("Inconsistent Mask Size: bad data?")); |
---|
| 4641 | } |
---|
| 4642 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
| 4643 | if (startIndices[i] > endIndices[i]) { |
---|
| 4644 | throw(AipsError("Mask start index > mask end index")); |
---|
[2012] | 4645 | } |
---|
| 4646 | } |
---|
| 4647 | |
---|
[2047] | 4648 | out.clear(); |
---|
| 4649 | for (uInt i = 0; i < startIndices.size(); ++i) { |
---|
| 4650 | out.push_back(startIndices[i]); |
---|
| 4651 | out.push_back(endIndices[i]); |
---|
| 4652 | } |
---|
| 4653 | |
---|
[2012] | 4654 | return out; |
---|
| 4655 | } |
---|
| 4656 | |
---|
[2161] | 4657 | vector<float> Scantable::getTsysSpectrum( int whichrow ) const |
---|
| 4658 | { |
---|
| 4659 | Vector<Float> tsys( tsysCol_(whichrow) ) ; |
---|
| 4660 | vector<float> stlTsys ; |
---|
| 4661 | tsys.tovector( stlTsys ) ; |
---|
| 4662 | return stlTsys ; |
---|
| 4663 | } |
---|
[2012] | 4664 | |
---|
[2591] | 4665 | vector<uint> Scantable::getMoleculeIdColumnData() const |
---|
| 4666 | { |
---|
| 4667 | Vector<uInt> molIds(mmolidCol_.getColumn()); |
---|
| 4668 | vector<uint> res; |
---|
| 4669 | molIds.tovector(res); |
---|
| 4670 | return res; |
---|
| 4671 | } |
---|
[2012] | 4672 | |
---|
[2591] | 4673 | void Scantable::setMoleculeIdColumnData(const std::vector<uint>& molids) |
---|
| 4674 | { |
---|
| 4675 | Vector<uInt> molIds(molids); |
---|
| 4676 | Vector<uInt> arr(mmolidCol_.getColumn()); |
---|
| 4677 | if ( molIds.nelements() != arr.nelements() ) |
---|
| 4678 | throw AipsError("The input data size must be the number of rows."); |
---|
| 4679 | mmolidCol_.putColumn(molIds); |
---|
[1907] | 4680 | } |
---|
[2591] | 4681 | |
---|
| 4682 | |
---|
| 4683 | } |
---|
[1819] | 4684 | //namespace asap |
---|